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		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696403</id>
		<title>Rep:Modxl9814</title>
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		<updated>2018-04-26T12:09:40Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Mean Squared Displacement */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696402</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696402"/>
		<updated>2018-04-26T12:08:54Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Atomic Forces */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696330</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696330"/>
		<updated>2018-04-20T17:57:00Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Structural properties and the radial distribution function */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696329</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696329"/>
		<updated>2018-04-20T17:56:31Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Structural properties and the radial distribution function */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696328</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696328"/>
		<updated>2018-04-20T17:55:51Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Plotting the Equations of State */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696327</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696327"/>
		<updated>2018-04-20T17:54:59Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Barostat and Thermostat */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696326</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696326"/>
		<updated>2018-04-20T17:52:02Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Heat Capacity Calculation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696325</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696325"/>
		<updated>2018-04-20T17:49:05Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Atomic Forces */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696238</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696238"/>
		<updated>2018-04-14T06:07:52Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Reduced Units */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696237</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696237"/>
		<updated>2018-04-14T06:06:14Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Atomic Forces */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
With &amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;, the LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696172</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696172"/>
		<updated>2018-04-06T13:17:57Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Atomic Forces */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r_{eq})=4\varepsilon(\frac{\sigma^{12}}{4\sigma^{12}}-\frac{\sigma^6}{2\sigma^6})=4\varepsilon(-\frac{1}{4})=-\varepsilon&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2^{11}}-\frac{4}{5}\times\frac{1}{2^5}=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2.5^{11}}-\frac{4}{5}\times\frac{1}{2.5^5}=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{3^{11}}-\frac{4}{5}\times\frac{1}{3^5}=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696171</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696171"/>
		<updated>2018-04-06T11:47:32Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
The Lennard-Jones potential can tell the potential energy of the interaction between two uncharged atoms. It can be expressed in (12,6) form:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r)=4\varepsilon(\frac{\sigma^{12}}{r^{12}}-\frac{\sigma^6}{r^6})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In this equation,&amp;lt;math&amp;gt;\varepsilon&amp;lt;/math&amp;gt; is the potential well depth,&amp;lt;math&amp;gt;\sigma&amp;lt;/math&amp;gt; is the distance where the potential between the pair of particles is zero and r is the distance between the pair of particles.&lt;br /&gt;
&lt;br /&gt;
As force is the negative derivative of potential energy, the equation of force in terms of the Lennard-Jones potential is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F_i=-\frac{d\phi (r^N)}{dr_i}&amp;lt;/math&amp;gt;=&amp;lt;math&amp;gt;24\varepsilon[2(\frac{\sigma^{12}}{r_i ^{13}})-\frac{\sigma^6}{r_i ^7}]&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
When the potential energy is zero, &amp;lt;math&amp;gt;r_i=\sigma=r_0&amp;lt;/math&amp;gt;, therefore by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{r_0 ^{12}}{r_0 ^{13}})-\frac{r_0^6}{r_0 ^7}]=24\varepsilon[\frac{2}{r_0}-\frac{1}{r_0}]=\frac{24\varepsilon}{r_0}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The equilibrium is reached when the resultant force is zero, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}]=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Divide both sides by &amp;lt;math&amp;gt;\frac{\sigma^6}{r^7}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r_{eq})=4\varepsilon(\frac{\sigma^{12}}{4\sigma^{12}}-\frac{\sigma^6}{2\sigma^6})=4\varepsilon(-\frac{1}{4})=-\varepsilon&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2^{11}}-\frac{4}{5}\times\frac{1}{2^5}=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2.5^{11}}-\frac{4}{5}\times\frac{1}{2.5^5}=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{3^{11}}-\frac{4}{5}\times\frac{1}{3^5}=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696079</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696079"/>
		<updated>2018-04-02T12:34:48Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
The Lennard-Jones potential can tell the potential energy of the interaction between two uncharged atoms. It can be expressed in (12,6) form:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r)=4\varepsilon(\frac{\sigma^{12}}{r^{12}}-\frac{\sigma^6}{r^6})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In this equation,&amp;lt;math&amp;gt;\varepsilon&amp;lt;/math&amp;gt; is the potential well depth,&amp;lt;math&amp;gt;\sigma&amp;lt;/math&amp;gt; is the distance where the potential between the pair of particles is zero and r is the distance between the pair of particles.&lt;br /&gt;
&lt;br /&gt;
As force is the negative derivative of potential energy, the equation of force in terms of the Lennard-Jones potential is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F_i=-\frac{d\phi (r^N)}{dr_i}&amp;lt;/math&amp;gt;=&amp;lt;math&amp;gt;24\varepsilon[2(\frac{\sigma^{12}}{r_i ^{13}})-\frac{\sigma^6}{r_i ^7}]&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
When the potential energy is zero, &amp;lt;math&amp;gt;r_i=\sigma=r_0&amp;lt;/math&amp;gt;, therefore by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{r_0 ^{12}}{r_0 ^{13}})-\frac{r_0^6}{r_0 ^7}]=24\varepsilon[\frac{2}{r_0}-\frac{1}{r_0}]=\frac{24\varepsilon}{r_0}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The equilibrium is reached when the resultant force is zero, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}]=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Divide both sides by &amp;lt;math&amp;gt;\frac{\sigma^6}{r^7}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r_{eq})=4\varepsilon(\frac{\sigma^{12}}{4\sigma^{12}}-\frac{\sigma^6}{2\sigma^6})=4\varepsilon(-\frac{1}{4})=-\varepsilon&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2^{11}}-\frac{4}{5}\times\frac{1}{2^5}=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2.5^{11}}-\frac{4}{5}\times\frac{1}{2.5^5}=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{3^{11}}-\frac{4}{5}\times\frac{1}{3^5}=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The initial position of atom is &amp;lt;math&amp;gt;(0.5,0.5,0.5)&amp;lt;/math&amp;gt;. After it moves along the vector &amp;lt;math&amp;gt;(0.7,0.6,0.2)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(1.2,1.1,0.7)&amp;lt;/math&amp;gt;. Applying the periodic boundary of &amp;lt;math&amp;gt;(0,0,0)&amp;lt;/math&amp;gt; to &amp;lt;math&amp;gt;(1,1,1)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(0.2,0.1,0.7)&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero so the particles in this system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. Also, from Fig.8, the lower the density, the lower the heat capacity. This is because high density means the particles will be closer together and therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The radial distribution function is an indicator of how far we can find a nearest neighbour for a particle. These distances would relate to the phases of the systems. From Fig(9), the RDFs for the three systems are very different. The solid has the largest number of peaks, as solid has the highest density with fixed vibrating atoms in short and long range order, thus would find a neighbour from a particle from some kind of ordered peaks, with decreasing peak amplitude with r and 0 amplitude between peaks. Liquid followed by gas has less peaks. The solid phase has long and short range order and this can be indicated by the peaks. The short range order is shown by the first three peaks and the long range order is shown by the smaller peaks behind.&lt;br /&gt;
&lt;br /&gt;
The RDF of the gas phase has only one broad peak as in this phase particles are highly disordered therefore no short nor long range order.&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest, the second nearest and the third nearest neighbour of the reference particle and the lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696078</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696078"/>
		<updated>2018-04-01T17:22:31Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
The Lennard-Jones potential can tell the potential energy of the interaction between two uncharged atoms. It can be expressed in (12,6) form:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r)=4\varepsilon(\frac{\sigma^{12}}{r^{12}}-\frac{\sigma^6}{r^6})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In this equation,&amp;lt;math&amp;gt;\varepsilon&amp;lt;/math&amp;gt; is the potential well depth,&amp;lt;math&amp;gt;\sigma&amp;lt;/math&amp;gt; is the distance where the potential between the pair of particles is zero and r is the distance between the pair of particles.&lt;br /&gt;
&lt;br /&gt;
As force is the negative derivative of potential energy, the equation of force in terms of the Lennard-Jones potential is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F_i=-\frac{d\phi (r^N)}{dr_i}&amp;lt;/math&amp;gt;=&amp;lt;math&amp;gt;24\varepsilon[2(\frac{\sigma^{12}}{r_i ^{13}})-\frac{\sigma^6}{r_i ^7}]&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
When the potential energy is zero, &amp;lt;math&amp;gt;r_i=\sigma=r_0&amp;lt;/math&amp;gt;, therefore by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{r_0 ^{12}}{r_0 ^{13}})-\frac{r_0^6}{r_0 ^7}]=24\varepsilon[\frac{2}{r_0}-\frac{1}{r_0}]=\frac{24\varepsilon}{r_0}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The equilibrium is reached when the resultant force is zero, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}]=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Divide both sides by &amp;lt;math&amp;gt;\frac{\sigma^6}{r^7}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r_{eq})=4\varepsilon(\frac{\sigma^{12}}{4\sigma^{12}}-\frac{\sigma^6}{2\sigma^6})=4\varepsilon(-\frac{1}{4})=-\varepsilon&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2^{11}}-\frac{4}{5}\times\frac{1}{2^5}=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2.5^{11}}-\frac{4}{5}\times\frac{1}{2.5^5}=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{3^{11}}-\frac{4}{5}\times\frac{1}{3^5}=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The initial position of atom is &amp;lt;math&amp;gt;(0.5,0.5,0.5)&amp;lt;/math&amp;gt;. After it moves along the vector &amp;lt;math&amp;gt;(0.7,0.6,0.2)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(1.2,1.1,0.7)&amp;lt;/math&amp;gt;. Applying the periodic boundary of &amp;lt;math&amp;gt;(0,0,0)&amp;lt;/math&amp;gt; to &amp;lt;math&amp;gt;(1,1,1)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(0.2,0.1,0.7)&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero.This means that the particles in Ideal Gas system can be compressed to occupy a very small given volume and a very high density. However, in the Lennard-Jones model, the molecules will interact with each other and the repulsive force shoots up when the molecules come too close.&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig.7 that, comparing the two trends, heatcapacity increases with pressure. This is because at lower pressure, provided that the volume is large enough, the intermolecular distance is larger and the density will not change a lot by the distance between the particles.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. This indicates that heat capacity is proportional to energy as shown in the equation. Also, it is shown that the lower the density, the lower the heat capacity.This is because high density means the particles will be closer together with lower volume, therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The radial distribution function is an indicator of how far we can find a nearest neighbour for a particle. These distances would relate to the phases of the systems. From Fig(9), the RDFs for the three systems are very different. The solid has the largest number of peaks, as solid has the highest density with fixed vibrating atoms in short and long range order, thus would find a neighbour from a particle from some kind of ordered peaks, with decreasing peak amplitude with r and 0 amplitude between peaks. Liquid followed by gas has less peaks. The solid phase has long and short range order and this can be indicated by the peaks. The short range order is shown by the first three peaks and the long range order is shown by the smaller peaks behind.&lt;br /&gt;
&lt;br /&gt;
The RDF of the liquid phase also has decreasing peaks with r. The wider and less number of peaks mean that the liquid phase is more disordered. The three peaks indicate that the liquid phase only has short range order.&lt;br /&gt;
&lt;br /&gt;
The RDF of the gas phase has only one broad peak as in this phase particles are highly disordered therefore no short nor long range order.&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest neighbor of the referenced particle, the second and the third. The lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696077</id>
		<title>Rep:Modxl9814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Modxl9814&amp;diff=696077"/>
		<updated>2018-04-01T17:15:30Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;==Theory==&lt;br /&gt;
===Velocity Verlet Algorithm===&lt;br /&gt;
One way to solve Newton&#039;s Second law F=ma is the velocity-Verlet algorithm. By using a Taylor expansion,the atomic positions, velocities and accelerations can be approximated at time t with good precision. The position of atom i, at time t, is denoted by &amp;lt;math&amp;gt;x_i (t)&amp;lt;/math&amp;gt; and the velocity of the atom at time t is denoted by &amp;lt;math&amp;gt;v_i (t)&amp;lt;/math&amp;gt;. Position at the next timestep &amp;lt;math&amp;gt;t+\delta t&amp;lt;/math&amp;gt; can be expressed by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x_i(t+\delta t)=x_i(t)+\frac{dx_i (t)}{dt}\delta t+\frac{1}{2!}\frac{d^2x_i (t)}{dt^2}\delta t^2+\frac{1}{3!}\frac{d^3x_i (t)}{dt^3}\delta t^3+\Omicron(\delta t^4)\quad (1) \quad &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
A single timestep is expressed as:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t+\delta t)=x_t+v_t \delta t+\frac{1}{2}a_t \delta t^2\quad (2) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\delta t)=x_t+\frac{1}{2}(a_{t+\delta t}+a_t)\delta t\quad (3) \quad&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1.PNG|600x600px|thumb|center|Fig 1: Classically calculated positions vs. velocity verlet calculated positions]]&lt;br /&gt;
&lt;br /&gt;
The classical harmonic oscillator can be describe by &amp;lt;math&amp;gt;x(t)=Acos(\omega t+\phi)&amp;lt;/math&amp;gt;. The errors oscillate through 5 peaks in the simulated time. The plot of the total energy vs. time of the simulated system:&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 2.PNG|600px|thumb|center|Fig 2:Error vs. time]]                                                                                     &lt;br /&gt;
&lt;br /&gt;
The cumulative error over a constant interval of time is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;error(x(t_0 +n\delta t))=\Omicron (\delta t^2)&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;https://www.saylor.org/site/wp-content/uploads/2011/06/MA221-6.1.pdf&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Thus, it can be seen from this equation that the relation between the maxima of the error of the Velocity-Verlet algorithm and &amp;lt;math&amp;gt;\delta t&amp;lt;/math&amp;gt; is quadratically increasing. The graph of the maxima of error vs. time therefore can be fit into the quadratic equation in figure 2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The total energy of the oscillating system is the sum of the kinetic energy and the potential energy, with &amp;lt;math&amp;gt;E_k=\frac{1}{2}mv^2&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;E_p=\frac{1}{2}kx^2&amp;lt;/math&amp;gt;. In this case, m=1 and k=1, therefore the equation is &amp;lt;math&amp;gt;E=\frac{v^2+x^2}{2}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 3a.PNG|600px|thumb|left|Fig 3a:Energy vs. Time at 0.1 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|[[File:Fig 3b.PNG|600px|thumb|left|Fig 3b:Energy vs. Time at 0.2 timestep with error limites of 0.5% on either side]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
In order for the total energy not to change by more than 1% over the course of the &#039;&#039;simulation&#039;&#039;, the timestep needs to be 0.2. It is important to monitor the total energy of the system to ensure that energy conservation is obeyed, the same as the real system.&lt;br /&gt;
&lt;br /&gt;
===Atomic Forces===&lt;br /&gt;
The Lennard-Jones potential can tell the potential energy of the interaction between two uncharged atoms. It can be expressed in (12,6) form:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r)=4\varepsilon(\frac{\sigma^{12}}{r^{12}}-\frac{\sigma^6}{r^6})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In this equation,&amp;lt;math&amp;gt;\varepsilon&amp;lt;/math&amp;gt; is the potential well depth,&amp;lt;math&amp;gt;\sigma&amp;lt;/math&amp;gt; is the distance where the potential between the pair of particles is zero and r is the distance between the pair of particles.&lt;br /&gt;
&lt;br /&gt;
As force is the negative derivative of potential energy, the equation of force in terms of the Lennard-Jones potential is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F_i=-\frac{d\phi (r^N)}{dr_i}&amp;lt;/math&amp;gt;=&amp;lt;math&amp;gt;24\varepsilon[2(\frac{\sigma^{12}}{r_i ^{13}})-\frac{\sigma^6}{r_i ^7}]&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
When the potential energy is zero, &amp;lt;math&amp;gt;r_i=\sigma=r_0&amp;lt;/math&amp;gt;, therefore by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{r_0 ^{12}}{r_0 ^{13}})-\frac{r_0^6}{r_0 ^7}]=24\varepsilon[\frac{2}{r_0}-\frac{1}{r_0}]=\frac{24\varepsilon}{r_0}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The equilibrium is reached when the resultant force is zero, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;F=24\varepsilon[2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}]=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2(\frac{\sigma^{12}}{r^{13}})-\frac{\sigma^6}{r^7}=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Divide both sides by &amp;lt;math&amp;gt;\frac{\sigma^6}{r^7}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;2\frac{\sigma^6}{r^6}-1=0&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, the equilibrium separation is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;r_{eq} =\sqrt[6]{2}\sigma&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The LJpotential at &amp;lt;math&amp;gt;r_{eq}&amp;lt;/math&amp;gt; is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\phi(r_{eq})=4\varepsilon(\frac{\sigma^{12}}{4\sigma^{12}}-\frac{\sigma^6}{2\sigma^6})=4\varepsilon(-\frac{1}{4})=-\varepsilon&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\varepsilon=-\phi(r_{eq})&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}\varepsilon \sigma^{12}r^{-11}+\frac{4}{5}\varepsilon \sigma^{6}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\sigma=\varepsilon=1.0&amp;lt;/math&amp;gt;, therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \int\phi\left(r\right)\mathrm{d}r=-\frac{4}{11}r^{-11}+\frac{4}{5}r^{-5}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2^{11}}-\frac{4}{5}\times\frac{1}{2^5}=-2.48\times 10^{-2}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{2.5\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{2.5^{11}}-\frac{4}{5}\times\frac{1}{2.5^5}=-8.18\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\int_{3\sigma}^\infty \phi\left(r\right)\mathrm{d}r=\frac{4}{11}\times\frac{1}{3^{11}}-\frac{4}{5}\times\frac{1}{3^5}=-3.29\times 10^{-3}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Periodic Boundary Conditions===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;1 mL=1 cm^3&amp;lt;/math&amp;gt;. The density of water=&amp;lt;math&amp;gt;1 g/cm^3&amp;lt;/math&amp;gt; under standard consitions (298K, 1atm). So the total mass of 1 mL water= 1g. The number of moles of water molecules=&amp;lt;math&amp;gt;\frac{1}{M_{H_2 O}}=\frac{1g}{18g/mol}=0.056 moles&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore the total number of molecules in 1 mL of water=&amp;lt;math&amp;gt;n\times N_a =0.056\times 6.02\times 10^{23}=3.37\times 10^{22}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The volume of 10,000 molecules of water=&amp;lt;math&amp;gt;\frac{10000}{3.37\times 10^{22}}=2.97\times 10^{-19}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The initial position of atom is &amp;lt;math&amp;gt;(0.5,0.5,0.5)&amp;lt;/math&amp;gt;. After it moves along the vector &amp;lt;math&amp;gt;(0.7,0.6,0.2)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(1.2,1.1,0.7)&amp;lt;/math&amp;gt;. Applying the periodic boundary of &amp;lt;math&amp;gt;(0,0,0)&amp;lt;/math&amp;gt; to &amp;lt;math&amp;gt;(1,1,1)&amp;lt;/math&amp;gt;, the position should be &amp;lt;math&amp;gt;(0.2,0.1,0.7)&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Reduced Units===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;r=r^*\sigma =0.34\times 10^{-9}\times 3.2=1.09nm&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The well depth=&amp;lt;math&amp;gt;\varepsilon=120K\times K_B \times 10^{-3} \times 6.022\times 10^{23}=0.997 KJ/mol&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;T^*=1.5&amp;lt;/math&amp;gt;, therefore &amp;lt;math&amp;gt;T=T^*\times \frac{\varepsilon}{K_B}=1.5\times 120K=180K&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Equilibration==&lt;br /&gt;
&lt;br /&gt;
===Creating the simulation box===&lt;br /&gt;
&lt;br /&gt;
Giving atoms random starting coordinates may make two atoms generated too close together. This will cause the two atoms to collide and arise the repulsion between the two atoms. The repulsive force between the atoms will drive them apart, leading to increase in the potential energy of the system and making it very unstable.&lt;br /&gt;
&lt;br /&gt;
A face-centered cubic lattice has 4 lattice points per unit cell. The side length of the cubic unit cell=&amp;lt;math&amp;gt; \sqrt[3]{\frac{4}{1.2}}= 1.49&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If 1000 unit cells were generated by the create_atoms command, 4000 atoms would be generated for a FCC lattice.&lt;br /&gt;
&lt;br /&gt;
===Setting the properties of the atoms===&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;Mass 1 1.0&amp;lt;/pre&amp;gt; &lt;br /&gt;
This means the mass of the single type of atom is 1.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_style lj/cut 3.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;Pair_style&amp;quot; indicates that the interaction is pairwise interaction. &amp;quot;lj.cut&amp;quot; describes the standard 12/6 Lennard-Jones potential without a Coulombic pairwise interaction. &amp;quot;3.0&amp;quot; indicates that the global cutoff for atoms is at 3.0.&lt;br /&gt;
&amp;lt;pre&amp;gt;Pair_coeff * *1.0 1.0&amp;lt;/pre&amp;gt;&lt;br /&gt;
&amp;quot;pair_coeff&amp;quot; specifies the pairwise force field coefficients. The two asterisks indicate that the command will apply to all atoms.&lt;br /&gt;
&lt;br /&gt;
If &amp;lt;math&amp;gt;x_i&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;v_i&amp;lt;/math&amp;gt;are specified,the Velocity-Verlet algorithm will be used for this simulation.&lt;br /&gt;
&lt;br /&gt;
===Running the simulation===&lt;br /&gt;
&lt;br /&gt;
The purpose of defining variable is that we don&#039;t need to manually change the numerical timestep each time the timestep needs to be changed. This reduces the human errors that may occur as the timestep only needs to be changed once to the value defined.&lt;br /&gt;
&lt;br /&gt;
===Checking equilibration===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 4a1.PNG|450px|thumb|left|Fig 4a:Total energy vs. time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4b1.PNG|450px|thumb|center|Fig 4b: Temperature vs Time at 0.001 timestep]]&lt;br /&gt;
||[[File:Fig 4c1.PNG|450px|thumb|right|Fig 4c: Pressure vs. Time at 0.001 timestep]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The simulation reaches equilibrium at 0.001 timestep as pressure and temperature become constant. It can be seen from pressure and temperature data that the simulation reaches equilibrium at t=0.29.The average pressure value is about 2.61 and the average temperature value is about 1.26.&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 4d.PNG|500px|thumb|center|Fig.5: Graph of energies for all timesteps]]&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig 5 that the total energy produced by 0.0025 timestep are very close to those produced by 0.001 timestep. Simulations at 0.0075 and 0.01 also reach equilibrium but the total energies are higher than those produced by 0.001 timestep, thus these timesteps are not very accurate. Therefore the largest timestep to get acceptable results is 0.0025 and the worst choice is 0.015 timestep as the simulation doesn&#039;t reach equilibrium.&lt;br /&gt;
&lt;br /&gt;
==Running simulations under specific conditions==&lt;br /&gt;
===Barostat and Thermostat===&lt;br /&gt;
In the system with N atoms, with 3 degrees of freedom:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;E_K = \frac{3}{2} N k_B T&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i v_i^2 = \frac{3}{2} N k_B T (1)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Multiplying every velocity by &amp;lt;math&amp;gt;\gamma&amp;lt;/math&amp;gt; and substituting T with &amp;lt;math&amp;gt;\mathfrak{T}&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (\gamma v_i)^2 = \frac{3}{2} N k_B \mathfrak{T} (2)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{1}{2}\sum_i m_i (v_i)^2 \times \gamma^2  = \frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Substituting (2):&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\frac{3}{2} N k_B T \times \gamma^2 =\frac{3}{2} N k_B \mathfrak{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;\gamma^2 = \frac{\mathfrak{T}}{T}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt; \gamma= \sqrt{\frac{\mathfrak{T}}{T}}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Examining the Input Script===&lt;br /&gt;
The numbers 100 1000 100000 indicate the timesteps the input values will be used to compute the averages of density, pressure and temperature. For this simulation, the average will be calculated using values produced by timestep 100,200,...100000. Therefore, 1000 values will be used to calculate the average. The following line tells LAMMPS to run the simulation for 100000 timesteps. 0.0025 timestep will be used. Therefore 250 time units are simulated.&lt;br /&gt;
&lt;br /&gt;
===Plotting the Equations of State===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 5a.PNG|450px|thumb|left|Fig.6:Density vs Temperature and Ideal Gas law at p=2.3 and p=2.6]]&lt;br /&gt;
|[[File:Fig 6b.PNG|450px|thumb|left|Fig.7:Density calculated by Ideal Gas Law compared to LJ model at P=2.3 and P=2.6]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Simulations were conducted at temperatures 2,2.5,3,3.5,5 and pressures 2.3 and 2.6.&lt;br /&gt;
&lt;br /&gt;
Density can also be calculated by Ideal Gas Law &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt; through the following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\frac{N}{V^*}=N\frac{\sigma ^3}{V}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;\frac{N}{V}=\frac{P}{k_BT}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;P=P^*\frac{\varepsilon}{\sigma ^3}&amp;lt;/math&amp;gt; and &amp;lt;math&amp;gt;T=T^*\frac{\varepsilon}{K_B}&amp;lt;/math&amp;gt;&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://www4.ncsu.edu/~franzen/public_html/CH795N/modules/ar_mod/comp_output.html&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;, by substitution we can get:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\rho^*=\sigma ^3 \frac{P}{k_BT}=\sigma ^3 \frac{P^*\frac{\varepsilon}{\sigma ^3}}{k_BT^*\frac{\varepsilon}{K_B}}=\frac{P^*}{T^*}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fig.7 shows that the simulated density is much lower than the density obtained by the Ideal Gas Law. This is because the Ideal Gas Law assumes that the molecules do not interact with each other and the repulsive force between the molecules is zero.This means that the particles in Ideal Gas system can be compressed to great extent, making the volume occupied very small for a given volume. Therefore the density is higher. In the Lennard-Jones model, the molecules will interact with each other and the repulsive force is greater when the distance between the molecules is smaller.&lt;br /&gt;
&lt;br /&gt;
It can be seen from Fig.7 that, comparing the two trends, heatcapacity increases with pressure. This is because at lower pressure, provided that the volume is large enough, the intermolecular distance is larger and the density will not change a lot by the distance between the particles.&lt;br /&gt;
&lt;br /&gt;
==Heat Capacity Calculation==&lt;br /&gt;
In the NVT ensemble, pressures (0.2,0.8) and temperatures (2,2.2,2.4,2.6,2.8) were used to calculate the heat capacity by using the following equation:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The code to run the simulation in the NVT ensemble is as following:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;variable density equal 0.2&lt;br /&gt;
&lt;br /&gt;
### DEFINE SIMULATION BOX GEOMETRY ###&lt;br /&gt;
lattice sc ${density}&lt;br /&gt;
region box block 0 15 0 15 0 15&lt;br /&gt;
create_box 1 box&lt;br /&gt;
create_atoms 1 box&lt;br /&gt;
&lt;br /&gt;
### DEFINE PHYSICAL PROPERTIES OF ATOMS ###&lt;br /&gt;
mass 1 1.0&lt;br /&gt;
pair_style lj/cut/opt 3.0&lt;br /&gt;
pair_coeff 1 1 1.0 1.0&lt;br /&gt;
neighbor 2.0 bin&lt;br /&gt;
&lt;br /&gt;
### SPECIFY THE REQUIRED THERMODYNAMIC STATE ###&lt;br /&gt;
variable T equal 2.0&lt;br /&gt;
variable p equal 4&lt;br /&gt;
variable timestep equal 0.0025&lt;br /&gt;
&lt;br /&gt;
### ASSIGN ATOMIC VELOCITIES ###&lt;br /&gt;
velocity all create ${T} 12345 dist gaussian rot yes mom yes&lt;br /&gt;
&lt;br /&gt;
### SPECIFY ENSEMBLE ###&lt;br /&gt;
timestep ${timestep}&lt;br /&gt;
fix nve all nve&lt;br /&gt;
&lt;br /&gt;
### THERMODYNAMIC OUTPUT CONTROL ###&lt;br /&gt;
thermo_style custom time etotal temp press&lt;br /&gt;
thermo 10&lt;br /&gt;
&lt;br /&gt;
### RECORD TRAJECTORY ###&lt;br /&gt;
dump traj all custom 1000 output-1 id x y z&lt;br /&gt;
&lt;br /&gt;
### SPECIFY TIMESTEP ###&lt;br /&gt;
&lt;br /&gt;
### RUN SIMULATION TO MELT CRYSTAL ###&lt;br /&gt;
run 10000&lt;br /&gt;
unfix nve&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### BRING SYSTEM TO REQUIRED STATE ###&lt;br /&gt;
variable tdamp equal ${timestep}*100&lt;br /&gt;
variable pdamp equal ${timestep}*1000&lt;br /&gt;
fix nvt all nvt temp ${T} ${T} ${tdamp} &lt;br /&gt;
run 10000&lt;br /&gt;
reset_timestep 0&lt;br /&gt;
&lt;br /&gt;
### MEASURE SYSTEM STATE ###&lt;br /&gt;
thermo_style custom step etotal temp press atoms density vol&lt;br /&gt;
variable dens equal density&lt;br /&gt;
variable dens2 equal density*density&lt;br /&gt;
variable temp equal temp&lt;br /&gt;
variable volume equal vol&lt;br /&gt;
variable temp2 equal temp*temp&lt;br /&gt;
variable press equal press&lt;br /&gt;
variable press2 equal press*press&lt;br /&gt;
variable N2 equal atoms*atoms&lt;br /&gt;
variable E2 equal etotal*etotal&lt;br /&gt;
variable E equal etotal&lt;br /&gt;
fix aves all ave/time 100 1000 100000 v_dens v_temp v_press v_dens2 v_temp2 v_press2 v_E v_E2&lt;br /&gt;
unfix nvt&lt;br /&gt;
fix nve all nve&lt;br /&gt;
run 100000&lt;br /&gt;
&lt;br /&gt;
variable avedens equal f_aves[1]&lt;br /&gt;
variable avetemp equal f_aves[2]&lt;br /&gt;
variable avepress equal f_aves[3]&lt;br /&gt;
variable errdens equal sqrt(f_aves[4]-f_aves[1]*f_aves[1])&lt;br /&gt;
variable errtemp equal sqrt(f_aves[5]-f_aves[2]*f_aves[2])&lt;br /&gt;
variable errpress equal sqrt(f_aves[6]-f_aves[3]*f_aves[3])&lt;br /&gt;
variable heatcapacity equal ${N2}*(f_aves[8]-f_aves[7]*f_aves[7])/f_aves[5]&lt;br /&gt;
variable CV equal ${heatcapacity}/${volume}&lt;br /&gt;
&lt;br /&gt;
print &amp;quot;Averages&amp;quot;&lt;br /&gt;
print &amp;quot;--------&amp;quot;&lt;br /&gt;
print &amp;quot;Density: ${avedens}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errdens}&amp;quot;&lt;br /&gt;
print &amp;quot;Temperature: ${avetemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errtemp}&amp;quot;&lt;br /&gt;
print &amp;quot;Pressure: ${avepress}&amp;quot;&lt;br /&gt;
print &amp;quot;Stderr: ${errpress}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity: ${heatcapacity}&amp;quot;&lt;br /&gt;
print &amp;quot;volume: ${volume}&amp;quot;&lt;br /&gt;
print &amp;quot;heatcapacity/volume: ${CV}&amp;quot;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8a3.PNG|500px|thumb|center|Fig.8: Cv/V vs. temperature at densities 0.2 and 0.8]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\frac{C_V}{V}&amp;lt;/math&amp;gt; was plotted against temperature. The volume for &amp;lt;math&amp;gt;\rho=0.2&amp;lt;/math&amp;gt; is 16875. The volume for &amp;lt;math&amp;gt;\rho=0.8&amp;lt;/math&amp;gt; is 4218.75. The heat capacity is inversely proportional to temperature from Fig.8, the same as shown in the equation &amp;lt;math&amp;gt;C_V = \frac{\partial E}{\partial T} = \frac{\mathrm{Var}\left[E\right]}{k_B T^2} = N^2\frac{\left\langle E^2\right\rangle - \left\langle E\right\rangle^2}{k_B T^2}&amp;lt;/math&amp;gt;. This is because the lattice energy gap decreases with increasing temperature, so less energy will be required. This indicates that heat capacity is proportional to energy as shown in the equation. Also, it is shown that the lower the density, the lower the heat capacity.This is because high density means the particles will be closer together with lower volume, therefore less heat is required to heat the system. For the same number of particles, if the density is lower, that means the volume the particles take up is larger. Therefore the heat required is higher .&lt;br /&gt;
&lt;br /&gt;
==Structural properties and the radial distribution function==&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 8.PNG|500px|thumb|left|Fig.9: g(r) vs. r for solid, liquid and gaseous phases ]]&lt;br /&gt;
&lt;br /&gt;
The radial distribution function was plotted for vapour, liquid and solid phases(Fig.9). The densities and temperatures were chosen from the phase diagram for the Lennard-Jones diagram.&amp;lt;ref&amp;gt;&amp;lt;nowiki&amp;gt;http://journals.aps.org/pr/abstract/10.1103/PhysRev.184.151&amp;lt;/nowiki&amp;gt;&amp;lt;/ref&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Phase&lt;br /&gt;
!Density&lt;br /&gt;
!Temperature&lt;br /&gt;
|-&lt;br /&gt;
|Vapour&lt;br /&gt;
|0.1&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Liquid&lt;br /&gt;
|0.8&lt;br /&gt;
|1.2&lt;br /&gt;
|-&lt;br /&gt;
|Solid&lt;br /&gt;
|1.6&lt;br /&gt;
|1.2&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The radial distribution function is an indicator of how far we can find a nearest neighbour for a particle. These distances would relate to the phases of the systems. From Fig(9), the RDFs for the three systems are very different. The solid has the largest number of peaks, as solid has the highest density with fixed vibrating atoms in short and long range order, thus would find a neighbour from a particle from some kind of ordered peaks, with decreasing peak amplitude with r and 0 amplitude between peaks. Liquid followed by gas has less peaks. The solid phase has long and short range order and this can be indicated by the peaks. The short range order is shown by the first three peaks and the long range order is shown by the smaller peaks behind.&lt;br /&gt;
&lt;br /&gt;
The RDF of the liquid phase also has decreasing peaks with r. The wider and less number of peaks mean that the liquid phase is more disordered. The three peaks indicate that the liquid phase only has short range order.&lt;br /&gt;
&lt;br /&gt;
The RDF of the gas phase has only one broad peak as in this phase particles are highly disordered therefore no short nor long range order.&lt;br /&gt;
&lt;br /&gt;
The first three peaks in solid RDF correspond to the nearest neighbor of the referenced particle, the second and the third. The lattice spacing is the distance between the zero probability minima, and it is in reduced units(Fig (10)).&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 1010.PNG|500px|thumb|center|Fig.10: Integral of g(r) vs. interatomic distance for solid phase ]]&lt;br /&gt;
&lt;br /&gt;
The coordination number for the first three peaks can be calculated from the plot of the integral of g(r) against interatomic distance. The integral of g(r) at the inflection points represent the coordination number of the three nearest neighbors. As a FCC lattice is used in a solid system, there should be 12 neighboring particles around each particle (shown at r=1.275). So the coordination number of the first peak is 12.  The next inflection number has a g(r) integral of 18. As it is a running integral, the coordination number of the second peak is &amp;lt;math&amp;gt;18-12=6&amp;lt;/math&amp;gt;. The coordination number of the third peak is &amp;lt;math&amp;gt;42-18=24&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Dynamical properties and the diffusion coefficient==&lt;br /&gt;
===Mean Squared Displacement===&lt;br /&gt;
The mean squared displacement is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;{\displaystyle {\rm {MSD}}\equiv \langle (x-x_{0})^{2}\rangle ={\frac {1}{N}}\sum _{n=1}^{N}(x_{n}(t)-x_{n}(0))^{2}}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a1.PNG|450px|thumb|left|Fig 11a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 11a.PNG|450px|thumb|left|Fig 11b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12a.PNG|450px|thumb|left|Fig 11c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 10a.PNG|450px|thumb|left|Fig 12a: Liquid simulation at d=0.8, T=1.2]]&lt;br /&gt;
||[[File:Fig 10b.PNG|450px|thumb|left|Fig 12b: Gas simulation at d=0.1, T=1.2]]&lt;br /&gt;
||[[File:Fig 12b.PNG|450px|thumb|left|Fig 12c: Solid simulation at d=1.6, T=1.2]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For the liquid phase, MSD is directly proportional to timestep for the liquid phase as the atoms move in Brownian motion. For gaseous phase, the first partis curved and the second part (above 2000) is linear. The curved part is because the particles move randomly in the system and the distance between them is very large. The frequency of collision between the particles is very low and thus the velocity of the atoms will be almost constant. The distance travelled per unit time is constant, thus MSD is proportional to &amp;lt;math&amp;gt;t^2&amp;lt;/math&amp;gt;. As longer time is simulated, collisions will occur more frequently and the motion can be described by brownian motion and MSD changes linearly with timestep. For solid phase, the particles only vibrate in fixed positions and do not have enough kinetic energy to diffuse, thus MSD reaches at constant value at around timestep 200.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is given by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D=\frac{1}{6}\frac{\delta\langle r^2\rangle}{\delta t}&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\delta\langle r^2\rangle&amp;lt;/math&amp;gt; is the slope of the trendline of the mean squared displacement vs. timestep plot. The timestep &amp;lt;math&amp;gt;\delta t=0.002&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For small system of 3375 atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0245}{0.002}=2.042&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For large system of 1 million atoms, the diffusion coefficient is:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.001}{0.002}=0.083&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{0.0305}{0.002}=2.542&amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D=\frac{1}{6} \times \frac{6 \times 10^{-8}}{0.002}=5 \times 10^{-6}&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
All of the diffusion coefficients are in reduced units. The coefficients for the larger system were similar to the ones for the smaller system.&lt;br /&gt;
&lt;br /&gt;
===Velocity Autocorrelation Function===&lt;br /&gt;
The equation of the position of a 1D harmonic oscillator is:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;x(t) = A\cos(\omega t + \phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;v(t)=\frac{dx}{dt}&amp;lt;/math&amp;gt;, thus:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t) = \frac{d(Acos(\omega t +\phi)}{dt}=-A\omega sin(\omega t+\phi)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
and&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;v(t+\tau)=-A\omega sin(\omega(t + \tau) +\phi) &amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Therefore, by substitution:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty} v(t)v(t + \tau)\mathrm{d}t}{\int_{-\infty}^{\infty} v^2(t)\mathrm{d}t}= \frac{\int_{-\infty}^{\infty} -A\omega sin(\omega t+ \phi) \times -A\omega sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} (-A\omega sin(\omega t+\phi))^2\mathrm{d}t}=\frac{(A\omega)^2 \int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{(A\omega)^2 \int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{\int_{-\infty}^{\infty} sin(\omega t+\phi) sin(\omega(t + \tau) +\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(x+y)=sin(x)cos(y)+cos(x)sin(y)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = \frac{\int_{-\infty}^{\infty}sin(\omega t+\phi)[sin(\omega t+ \phi)cos(\omega \tau)+cos(\omega t+\phi)sin(\omega \tau)]\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}=\frac{cos(\omega \tau)\int_{-\infty}^{\infty}sin^2(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t} = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty}sin(\omega t+ \phi)cos(\omega t+\phi)\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Since &amp;lt;math&amp;gt;sin(2x)=2sin(x)cos(x)&amp;lt;/math&amp;gt;:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau) = cos(\omega \tau)+\frac{sin(\omega \tau)\int_{-\infty}^{\infty} \frac{1}{2}sin(2(\omega t+ \phi))\mathrm{d}t}{\int_{-\infty}^{\infty} sin^2(\omega t+\phi)\mathrm{d}t}&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
As &amp;lt;math&amp;gt;sin(x)&amp;lt;/math&amp;gt; is an odd function, the area above the x-axis and below the x-axis cancel out from negative infinity to positive infinity. Thus, &amp;lt;math&amp;gt;\int_{-\infty}^{\infty} sin(2(\omega t+\phi))=0&amp;lt;/math&amp;gt;. therefore:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;center&amp;gt;&amp;lt;math&amp;gt;C(\tau)=cos(\omega \tau)&amp;lt;/math&amp;gt;&amp;lt;/center&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Fig 13.PNG|500px|thumb|center|Fig.14: VACF for solid, liquid and 1D Harmonic Oscillator]]&lt;br /&gt;
&lt;br /&gt;
The minima in the VACF for the liquid system represent the collisions between the atoms and the solvent molecules and change in direction. The minima in the VACF for the solid system represent the collisions between the atoms and change in direction. The minima for the solid system is lower than the minima for the liquid system because of the stronger interatomic forces. The VACF for the liquid system only has one weak oscillation, this is because the atoms only interact with their closest neighbor. In the VACF for the solid system, there are more oscillations as the atoms can vibrate in fixed positions. The harmonic oscillator VACF is very different to the Lennard Jones liquid and solid as there are no interactions between the atoms so the atoms will always vibrate with constant velocity without loss in energy. Therefore, the amplitude doe not change.&lt;br /&gt;
&lt;br /&gt;
By applying the trapezium rule, integral under VACF can be calculated and running integral can be plotted:&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 15a1.PNG|450px|thumb|left|Fig.15a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 15b1.PNG|450px|thumb|left|Fig.15b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 15c.PNG|450px|thumb|left|Fig.15c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Fig 16a1.PNG|450px|thumb|left|Fig.16a: running integral vs. time for liquid]]&lt;br /&gt;
||[[File:Fig 16b1.PNG|450px|thumb|left|Fig.16b: running integral vs. time for solid]]&lt;br /&gt;
||[[File:Fig 16c.PNG|450px|thumb|left|Fig.16c: running integral vs. time for gas]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient is calculated by:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;D = \frac{1}{3}\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The last point of the running integral is &amp;lt;math&amp;gt;\int_0^\infty \mathrm{d}\tau \left\langle\mathbf{v}\left(0\right)\cdot\mathbf{v}\left(\tau\right)\right\rangle &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
For 3375 atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2937=9.79 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 5.64 \times 10^{-4}=1.88 \times 10{-4}&amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 7.054=2.351&amp;lt;/math&amp;gt;;&lt;br /&gt;
&lt;br /&gt;
For 1 million atoms:&lt;br /&gt;
Liquid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 0.2703=9.01 \times 10^{-2} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Solid: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 1.37 \times 10^{-4}=4.57 \times 10^{-5} &amp;lt;/math&amp;gt;;&lt;br /&gt;
Gas: &amp;lt;math&amp;gt;D= \frac{1}{3} \times 9.805=3.268&amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The diffusion coefficient calculated from this method was largest for gas, followed by liquid and then gas. The coefficients for the larger system were very similar to the ones for the smaller system. The coefficients calculated by MSD were similar to the ones calculated by VACF for liquid and gas, but the coefficient calculated by VACF was larger than the one calculated by MSD for solid. The largest source of error may be that the trapezium rule overestimates the area under the solid curve as the timestep is not small enough.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611720</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611720"/>
		<updated>2017-03-24T11:57:19Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Abstract==&lt;br /&gt;
In this experiment, the thermal expansion of the lattice structure MgO was computed by two methods: the Quasi-harmonic approximation and the Molecular Dynamics. The experiment was done over the temperature range 0k-1000K in steps of 100K and the grid size used was 32x32x32. The Molecular dynamics method works better at high temperture and the quasi-harmonic approximation works better at low temperature. The molecular dynamics method agrees better with the literature.&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Magnesium Oxide has a lot of refractory and electrical applications. It has good refractoriness, high thermal conductivity and low electrical conductivity.&amp;lt;ref&amp;gt;http://www.azom.com/article.aspx?ArticleID=54&amp;lt;/ref&amp;gt;Because of these properties,MgO can be used to investigate the thermal expansions of crystals. &lt;br /&gt;
&lt;br /&gt;
The fcc MgO system is assumed to have perfect crystal structure. MgO can be represented by two kinds of cell: the primitive cell which is the smallest cell which contains only one lattice point. The whole crystal of MgO could be built up by the repetitive arrangement of the smallest primitive unit cell; The conventional unit cell which is a cube with edge length with lattice parameter a and it contains 4 lattice points with 8x&amp;lt;math&amp;gt;\frac{1}{8}&amp;lt;/math&amp;gt; lattice points at the corners and 6x&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt; lattice points at the faces.&amp;lt;ref&amp;gt;http://www.physics-in-a-nutshell.com/article/11&amp;lt;/ref&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Primitiveliuliu.PNG|400px|thumb|left|Fig.1: Primitive Cell ]]&lt;br /&gt;
||[[File:Conventionalliuliu.PNG|400px|thumb|left|Fig.2:Conventional Cell ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The aim of this exercise is to investigate the thermal expansion property of MgO. DLVisualize which is a graphical interface used to visualize materials&#039; structures and properties, can use GULP on the linux system to do the classical simulation which is the Quasi-harmonic approximation, as well as the molecular dynamics. The thermal expansion simulation was carried out over the temperature range 0K to 1000K. The optimal grid size was found by simulating the density of states at different grid sizes and was found out to be 32x32x32. A smaller grid size will be inaccurate while a larger grid size will be time-consuming. The thermal expansion coefficient could be found by plotting the cell volume against temperature. The primitive cell was simulated by the quasi-harmonic approximation. The conventional cell which has 32 MgO units was simulated by Molecular Dynamics as it has larger system. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611696</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611696"/>
		<updated>2017-03-24T11:48:08Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Abstract==&lt;br /&gt;
In this experiment, the thermal expansion of the lattice structure MgO was computed by two methods: the Quasi-harmonic approximation and the Molecular Dynamics. The experiment was done over the temperature range 0k-1000K in steps of 100K and the grid size used was 32x32x32. The Molecular dynamics method works better at high temperture and the quasi-harmonic approximation works better at low temperature. The molecular dynamics method agrees better with the literature.&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Magnesium Oxide has a lot of refractory and electrical applications. It has good refractoriness, high thermal conductivity and low electrical conductivity.&amp;lt;ref&amp;gt;http://www.azom.com/article.aspx?ArticleID=54&amp;lt;/ref&amp;gt;Because of these properties,MgO can be used to investigate the thermal expansions of crystals. &lt;br /&gt;
&lt;br /&gt;
The fcc MgO system is assumed to have perfect crystal structure. MgO can be represented by two kinds of cell: the primitive cell which is the smallest cell which contains only one lattice point. The whole crystal of MgO could be built up by the repetitive arrangement of the smallest primitive unit cell; The conventional unit cell which is a cube with edge length with lattice parameter a and it contains 4 lattice points with 8x&amp;lt;math&amp;gt;\frac{1}{8}&amp;lt;/math&amp;gt; lattice points at the corners and 6x&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt; lattice points at the faces.&amp;lt;ref&amp;gt;http://www.physics-in-a-nutshell.com/article/11&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Primitiveliuliu.PNG|400px|thumb|left|Fig.1: Primitive Cell ]]&lt;br /&gt;
||[[File:Conventionalliuliu.PNG|400px|thumb|left|Fig.2:Conventional Cell ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The aim of this exercise is to investigate the thermal expansion property of MgO. DLVisualize which is a graphical interface used to visualize materials&#039; structures and properties, can use GULP on the linux system to do the classical simulation which is the Quasi-harmonic approximation, as well as the molecular dynamics. The thermal expansion simulation was carried out over the temperature range 0K to 1000K. The optimal grid size was found by simulating the density of states at different grid sizes and was found out to be 32x32x32. A smaller grid size will be inaccurate while a larger grid size will be time-consuming. The thermal expansion coefficient could be found by plotting the cell volume against temperature. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Conventionalliuliu.PNG&amp;diff=611694</id>
		<title>File:Conventionalliuliu.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Conventionalliuliu.PNG&amp;diff=611694"/>
		<updated>2017-03-24T11:47:51Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitiveliuliu.PNG&amp;diff=611692</id>
		<title>File:Primitiveliuliu.PNG</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitiveliuliu.PNG&amp;diff=611692"/>
		<updated>2017-03-24T11:47:28Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611675</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611675"/>
		<updated>2017-03-24T11:44:58Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Abstract==&lt;br /&gt;
In this experiment, the thermal expansion of the lattice structure MgO was computed by two methods: the Quasi-harmonic approximation and the Molecular Dynamics. The experiment was done over the temperature range 0k-1000K in steps of 100K and the grid size used was 32x32x32. The Molecular dynamics method works better at high temperture and the quasi-harmonic approximation works better at low temperature. The molecular dynamics method agrees better with the literature.&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Magnesium Oxide has a lot of refractory and electrical applications. It has good refractoriness, high thermal conductivity and low electrical conductivity.&amp;lt;ref&amp;gt;http://www.azom.com/article.aspx?ArticleID=54&amp;lt;/ref&amp;gt;Because of these properties,MgO can be used to investigate the thermal expansions of crystals. &lt;br /&gt;
&lt;br /&gt;
The fcc MgO system is assumed to have perfect crystal structure. MgO can be represented by two kinds of cell: the primitive cell which is the smallest cell which contains only one lattice point. The whole crystal of MgO could be built up by the repetitive arrangement of the smallest primitive unit cell; The conventional unit cell which is a cube with edge length with lattice parameter a and it contains 4 lattice points with 8x&amp;lt;math&amp;gt;\frac{1}{8}&amp;lt;/math&amp;gt; lattice points at the corners and 6x&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt; lattice points at the faces.&amp;lt;ref&amp;gt;http://www.physics-in-a-nutshell.com/article/11&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Primitive1.pdf|450px|thumb|left|Fig.1: Primitive Cell ]]&lt;br /&gt;
||[[File:Conventionalliu.pdf|450px|thumb|left|Fig.2:Conventional Cell ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The aim of this exercise is to investigate the thermal expansion property of MgO. DLVisualize which is a graphical interface used to visualize materials&#039; structures and properties, can use GULP on the linux system to do the classical simulation which is the Quasi-harmonic approximation, as well as the molecular dynamics. The thermal expansion simulation was carried out over the temperature range 0K to 1000K. The optimal grid size was found by simulating the density of states at different grid sizes and was found out to be 32x32x32. A smaller grid size will be inaccurate while a larger grid size will be time-consuming. The thermal expansion coefficient could be found by plotting the cell volume against temperature. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitive1.pdf&amp;diff=611671</id>
		<title>File:Primitive1.pdf</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitive1.pdf&amp;diff=611671"/>
		<updated>2017-03-24T11:44:32Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611662</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=611662"/>
		<updated>2017-03-24T11:42:59Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Abstract==&lt;br /&gt;
In this experiment, the thermal expansion of the lattice structure MgO was computed by two methods: the Quasi-harmonic approximation and the Molecular Dynamics. The experiment was done over the temperature range 0k-1000K in steps of 100K and the grid size used was 32x32x32. The Molecular dynamics method works better at high temperture and the quasi-harmonic approximation works better at low temperature. The molecular dynamics method agrees better with the literature.&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Magnesium Oxide has a lot of refractory and electrical applications. It has good refractoriness, high thermal conductivity and low electrical conductivity.&amp;lt;ref&amp;gt;http://www.azom.com/article.aspx?ArticleID=54&amp;lt;/ref&amp;gt;Because of these properties,MgO can be used to investigate the thermal expansions of crystals. &lt;br /&gt;
&lt;br /&gt;
The fcc MgO system is assumed to have perfect crystal structure. MgO can be represented by two kinds of cell: the primitive cell which is the smallest cell which contains only one lattice point. The whole crystal of MgO could be built up by the repetitive arrangement of the smallest primitive unit cell; The conventional unit cell which is a cube with edge length with lattice parameter a and it contains 4 lattice points with 8x&amp;lt;math&amp;gt;\frac{1}{8}&amp;lt;/math&amp;gt; lattice points at the corners and 6x&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt; lattice points at the faces.&amp;lt;ref&amp;gt;http://www.physics-in-a-nutshell.com/article/11&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Primitiveliu.pdf|450px|thumb|left|Fig.1: Primitive Cell ]]&lt;br /&gt;
||[[File:Conventionalliu.pdf|450px|thumb|left|Fig.2:Conventional Cell ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
The aim of this exercise is to investigate the thermal expansion property of MgO. DLVisualize which is a graphical interface used to visualize materials&#039; structures and properties, can use GULP on the linux system to do the classical simulation which is the Quasi-harmonic approximation, as well as the molecular dynamics. The thermal expansion simulation was carried out over the temperature range 0K to 1000K. The optimal grid size was found by simulating the density of states at different grid sizes and was found out to be 32x32x32. A smaller grid size will be inaccurate while a larger grid size will be time-consuming. The thermal expansion coefficient could be found by plotting the cell volume against temperature. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Conventionalliu.pdf&amp;diff=611660</id>
		<title>File:Conventionalliu.pdf</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Conventionalliu.pdf&amp;diff=611660"/>
		<updated>2017-03-24T11:42:05Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
&lt;hr /&gt;
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		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitiveliu.pdf&amp;diff=611655</id>
		<title>File:Primitiveliu.pdf</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitiveliu.pdf&amp;diff=611655"/>
		<updated>2017-03-24T11:41:20Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: &lt;/p&gt;
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	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610803</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610803"/>
		<updated>2017-03-24T03:31:28Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Abstract==&lt;br /&gt;
In this experiment, the thermal expansion of the lattice structure MgO was computed by two methods: the Quasi-harmonic approximation and the Molecular Dynamics. The experiment was done over the temperature range 0k-1000K in steps of 100K and the grid size used was 32x32x32. The Molecular dynamics method works better at high temperture and the quasi-harmonic approximation works better at low temperature. The molecular dynamics method agrees better with the literature.&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
Magnesium Oxide has a lot of refractory and electrical applications. It has good refractoriness, high thermal conductivity and low electrical conductivity.&amp;lt;ref&amp;gt;http://www.azom.com/article.aspx?ArticleID=54&amp;lt;/ref&amp;gt;Because of these properties,MgO can be used to investigate the thermal expansions of crystals. &lt;br /&gt;
&lt;br /&gt;
The fcc MgO system is assumed to have perfect crystal structure. MgO can be represented by two kinds of cell: the primitive cell which is the smallest cell which contains only one lattice point. The whole crystal of MgO could be built up by the repetitive arrangement of the smallest primitive unit cell; The conventional unit cell which is a cube with edge length with lattice parameter a and it contains 4 lattice points with 8x&amp;lt;math&amp;gt;\frac{1}{8}&amp;lt;/math&amp;gt; lattice points at the corners and 6x&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt; lattice points at the faces.&amp;lt;ref&amp;gt;http://www.physics-in-a-nutshell.com/article/11&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The aim of this exercise is to investigate the thermal expansion property of MgO. DLVisualize which is a graphical interface used to visualize materials&#039; structures and properties, can use GULP on the linux system to do the classical simulation which is the Quasi-harmonic approximation, as well as the molecular dynamics. The thermal expansion simulation was carried out over the temperature range 0K to 1000K. The optimal grid size was found by simulating the density of states at different grid sizes and was found out to be 32x32x32. A smaller grid size will be inaccurate while a larger grid size will be time-consuming. The thermal expansion coefficient could be found by plotting the cell volume against temperature. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610783</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610783"/>
		<updated>2017-03-24T01:51:15Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig.3: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Fig.4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Fig.4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Fig.4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Fig.5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Fig.5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 2: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.6: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.7: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.8: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.9: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.10: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig.8, it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig.9  and fig.10 , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.11: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.12: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig.12 shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610780</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610780"/>
		<updated>2017-03-24T01:40:59Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=Thermal expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610776</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610776"/>
		<updated>2017-03-24T01:39:28Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Conclusion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
Two methods were used to find the thermal expansion coefficients in this experiment: the quasi-harmonic approximation and the molecular dynamics. The grid size 32x32x32 was found to be optimal and was used in the quasi-harmonic approximation to find the relationship between the Helmholtz free energy, the lattice constant and the cell volume with temperature. The thermal expansion coefficient can be found by calculating the gradient of the cell volume against temperature graph. The molecular dynamics methods however relies on the equations of classical mechanics. The quasi-harmonic approximation works better at low temperature and the molecular dynamics method works better at high temperature. By comparison, the molecular dynamics method shows better agreement with the literature value.&lt;br /&gt;
&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610766</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610766"/>
		<updated>2017-03-24T01:12:50Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|right|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|right|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will no longer be perfect. Thus this does not follow the Quasi-harmonic approximation. Therefore, the quasi-harmonic approximation cannot be used at high temperature.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610762</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610762"/>
		<updated>2017-03-24T01:07:08Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|250px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|250px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|350px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|350px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|350px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610761</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610761"/>
		<updated>2017-03-24T01:05:57Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Phonon dispersion and Density of States */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|350x350px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|250px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|250px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|250px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|250px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|250px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|250px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|250px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610757</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610757"/>
		<updated>2017-03-24T01:02:57Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Results and Discussion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume at each temperature range by 32 which is the number of MgO units in the supercell, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the Molecular Dynamics method is more accurate than the quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610752</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610752"/>
		<updated>2017-03-24T00:56:44Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods, 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by the quasi-harmonic approximation, 2.6689x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; by MD. The thermal expansion coefficient calculated by the quasi-harmonic approximation is closer to the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Therefore, the quasi-harmonic approximation is more accurate than the Molecular Dynamics method.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610735</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610735"/>
		<updated>2017-03-24T00:50:43Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689 K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
Fig shows the comparison of MD and the quasi-harmonic approximation. The two curves have similar shapes. The cell volume predicted by MD lies below the one predicted by the quasi-harmonic approximation at each temperature from 0K to 1000K. The quasi-harmonic approximation works better at low tempwerature while becomes inaccurate at high temperature. This is because at high temperature, bond dissociation starts to happen and the crystal structure is no longer perfect. Therefore the quasi-harmonic approximation does not apply any more. The Molecular Dynamics methods works well at high temperature, however does not work at low temperature. This is because this method treats the system classically and depends on the velocity on each atom. At 0K, there is no result as atoms do not move at 0K. &lt;br /&gt;
&lt;br /&gt;
By comparing the thermal expansion coefficient calculated by the two methods,&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610681</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610681"/>
		<updated>2017-03-24T00:06:14Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. The first three points were not included as they did not show the linear relationship. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005.The trendline also did not include the first two points. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689 K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610524</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610524"/>
		<updated>2017-03-23T22:11:37Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely.&amp;lt;ref&amp;gt;https://web.stanford.edu/class/cs279/lectures/lecture4.pdf&amp;lt;/ref&amp;gt; The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689 K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610521</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610521"/>
		<updated>2017-03-23T22:09:12Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely. The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt; was 0.0005. By dividing the gradient by the initial volume which was 18.73463 Å³, the thermal expansion coefficient was found to be  2.6689 K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610503</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610503"/>
		<updated>2017-03-23T22:00:31Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely. The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig , &amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P was 0&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610502</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610502"/>
		<updated>2017-03-23T21:59:07Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The molecular dynamics method is used for a supercell having 32 MgO units. This method simulates how atoms move in real life and uses Newton&#039;s second law to determine how forces affect the motions of the atoms. The size of the cell needs to be large enough to insure that the atoms vibrate freely. The same grid size 32x32x32 was used. By dividing the last averaged volume on the same temperature range by 32, the cell volume can be found. From fig ,&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610374</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610374"/>
		<updated>2017-03-23T20:08:30Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Thermal expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 810 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; and 350 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610206</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610206"/>
		<updated>2017-03-23T17:57:02Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* Phonon dispersion and Density of States */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 2&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610202</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610202"/>
		<updated>2017-03-23T17:55:28Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha_v =\frac{1}{V}\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt; &#039;&#039;&#039;Equation 4&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;V&#039;&#039;&#039; is the initial volume of the cell,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;math&amp;gt;\left(\frac{\partial V}{\partial T}\right)_P &amp;lt;/math&amp;gt;&#039;&#039;&#039; is the gradient of the cell volume vs. temperature graph.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. From equation 4, by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610182</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610182"/>
		<updated>2017-03-23T17:39:53Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;F(TV)=U(V)-TS(T,V)&amp;lt;/math&amp;gt;  &#039;&#039;&#039;Equation 3&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
Where &#039;&#039;&#039;U&#039;&#039;&#039; is the internal lattice energy,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;T&#039;&#039;&#039; is the absolute temperature, &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;V&#039;&#039;&#039; is the volume,&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;S&#039;&#039;&#039; is the entropy due to the vibrational degrees of freedom.&amp;lt;ref&amp;gt;http://uspex.stonybrook.edu/qzhu-thesis/sect0027.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610168</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610168"/>
		<updated>2017-03-23T17:29:21Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610162</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610162"/>
		<updated>2017-03-23T17:27:01Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
As the temperature approaches the melting point of MgO, the phonon modes do not represent the actual motions of the ions. This is because the bonds will break at the melting point and the crystal structure will change. Thus this does not follow the Quasi-harmonic approximation.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610124</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610124"/>
		<updated>2017-03-23T17:12:20Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion.&amp;lt;ref&amp;gt;Vibrational Thermodynamics of Materials, Brent Fultz&lt;br /&gt;
California Institute of Technology, W. M. Keck Laboratory, Pasadena CA 91125 USA, July 6, 2009&amp;lt;/ref&amp;gt; At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610109</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610109"/>
		<updated>2017-03-23T17:06:26Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion. At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&amp;lt;ref&amp;gt;http://web.mit.edu/mbuehler/www/SIMS/Thermal%20Expansion.html&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K&amp;lt;ref&amp;gt;https://www.hindawi.com/journals/jther/2014/123478/&amp;lt;/ref&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610106</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610106"/>
		<updated>2017-03-23T17:04:00Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion. At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&amp;lt;ref&amp;gt;MSE 2090: Introduction to Materials Science Chapter 19, Thermal Properties&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This is smaller than the literature value 4x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; at 300K.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610026</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=610026"/>
		<updated>2017-03-23T16:31:30Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion. At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient &amp;lt;math&amp;gt;\alpha_v&amp;lt;/math&amp;gt; is 2.124x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=609995</id>
		<title>Rep:Mod:xl98149814</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:xl98149814&amp;diff=609995"/>
		<updated>2017-03-23T16:21:46Z</updated>

		<summary type="html">&lt;p&gt;Xl9814: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= &#039;&#039;Thermal expansion of MgO&#039;&#039; =&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
==Results and Discussion==&lt;br /&gt;
===Phonon dispersion and Density of States===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The phonon dispersion graph show 6 branches as there are 2 atoms per MgO molecule in 3 dimensions. &lt;br /&gt;
[[File:MgOphonondispersion1.PNG|600x600px|thumb|center|Fig 1: Phonon Dispersion curves of MgO]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! colspan=&amp;quot;8&amp;quot; |Figure 4: MgO &#039;&#039;&#039;phonon Density of States with different grid sizes&#039;&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|[[File:1..PNG|300px|thumb]]&lt;br /&gt;
|2x2x2&lt;br /&gt;
|[[File:2liu.PNG|300px|thumb]]&lt;br /&gt;
|4x4x4&lt;br /&gt;
|[[File:4liu.PNG|300px|thumb]]&lt;br /&gt;
|8x8x8&lt;br /&gt;
|[[File:8liu.PNG|300px|thumb]]&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|[[File:16.PNG|300px|thumb]]&lt;br /&gt;
|32x32x32&lt;br /&gt;
|[[File:32.PNG|300px|thumb]]&lt;br /&gt;
|64x64x64&lt;br /&gt;
|[[File:64.PNG|300px|thumb]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For the density of states of 1x1x1 grid, the k-point is the symmetry point L which is (&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;,&amp;lt;math&amp;gt;\frac{1}{2}&amp;lt;/math&amp;gt;). In the density of states graph of 1x1x1 grid, the intensity of the two lower frequency peaks (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; adn 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are twice as large as the intensity of the two higher frequency peaks (680 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 810 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;). From the dispersion curve, it can be seen that the symmetry point L contains exactly the same frequencies and the two lower frequency numbers (290 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt; and 350 &amp;lt;math&amp;gt;cm^{-1}&amp;lt;/math&amp;gt;) are doubly degenerate, which matches the intensity of the peaks in the DOS graph. This gives the same information as the DOS graph.&lt;br /&gt;
&lt;br /&gt;
The density of states increases with grid size as more k points are used to calculate the DOS. From Figure 4, it can be seen that there are only a few sharp peaks on the DOS graphs of 1x1x1, 2x2x2 and 4x4x4 grid sizes. This means only few frequencies are covered. As the grid size increases, more k-points in the reciprocal space are used to calculate the DOS, thus more frequencies are covered and overlap. This leads to a smoother DOS curve. The denser the grid, the smoother the DOS curve as more atoms are used in the calculation so more details are given. Therefore larger grid size can include more frequencies and thus give more accurate representation. From Figure 4, it can be seen that grid size 32x32x32 and 64x64x64 generate similar DOS curves. However, A grid size of 64x64x64 is very time consuming. Therefore the grid size 32x32x32 should be the minimum for a reasonable approximation to the density of states. &lt;br /&gt;
&lt;br /&gt;
The optimal grid size 32x32x32 can be used for CaO as CaO has similar structure with MgO. Faujasite has covalent bonding in its structure, therefore it has a larger cell than MgO. According to Equation 2, a smaller grid size should be used in the reciprocal space. As for a metal such as lithium, it has metallic bonding in its structure, therefore it has a smaller cell than MgO, thus a larger grid size should be used.   &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;a^*=\frac{2 \pi}{a}&amp;lt;/math&amp;gt; Equation 2&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free energy vs. grid size.PNG|600x600px|thumb|right|Figure 5: Helmholtz Free Energy vs. Grid size]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+Table 1:  Helmholtz Free energy vs. grid size&lt;br /&gt;
!Grid size&lt;br /&gt;
!Helmholtz Free Energy/ eV&lt;br /&gt;
!ΔA/ meV (compared with free energy of 64x64x64)&lt;br /&gt;
|-&lt;br /&gt;
|1x1x1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.930301&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-3.818&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|2x2x2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926609&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-0.126&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4x4x4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.92645&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.033&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8x8x8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926478&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.005&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16x16x16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926482&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.001&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32x32x32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64x64x64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.926483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;0.000&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Figure 5 shows that the Helmholtz Free Energy increases with grid size. This is because larger grid size means more k-points are taken to calculate the free energy and more accuracy is obtained. The Helmholtz Free Energy becomes stable from grid size 32x32x32. This further proves that 32x32x32 is the optimal grid size. From table 1, it is shown that grid size 2x2x2 is appropriate for a calculation accurate to 1 and 0.5 meV. Grid size 4x4x4 is appropriate for a calculation accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
Quasi-harmonic approximation is a phonon-based model that describes volume-dependent thermal expansion. At T=0K, the interatomic potential is harmonic and the average value of interatomic distance does not change. As temperature increases, the average amplitude of atomic vibrations also increases. This results in the increase of the average value of interatomic distance. In order to investigate the thermal expansion of MgO, the Helmholtz free energy, cell volume and lattice parameters were recorded from 0K to 1000K in steps of 100K (Table 2). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
Table 3: Effects of temperature on the Helmholtz free energy and the lattice constant&lt;br /&gt;
!Temperature/ K&lt;br /&gt;
!Helmholtz free energy/ eV&lt;br /&gt;
!Lattice constant/ Å&lt;br /&gt;
!Cell Volume/ Å³ &lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |0&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90190629&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.836496&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |100&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90241969&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.986563&lt;br /&gt;
  |18.838266&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |200&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.90937745&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.987604&lt;br /&gt;
  |18.856201&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |300&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.92812483&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.98939 &lt;br /&gt;
  |18.890025&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |400&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.95859432&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.991629&lt;br /&gt;
  |18.932506&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |500&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-40.99943614&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.994134&lt;br /&gt;
  |18.98011&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |600&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.04931565&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.99682&lt;br /&gt;
  |19.031221&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
  |700&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.1071195&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |2.999643&lt;br /&gt;
  |19.085056&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |800&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.17189216&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.002587&lt;br /&gt;
  |19.141316&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |900&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.24301846&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.005634&lt;br /&gt;
  |19.199638&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
  |1000&lt;br /&gt;
  |&amp;lt;nowiki&amp;gt;-41.31984872&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
  |3.008783&lt;br /&gt;
  |19.260042&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Harmonic.PNG|350px|thumb|left|Fig.2: Harmonic model ]]&lt;br /&gt;
||[[File:Thermal expansion.PNG|350px|thumb|left|Fig.4: anharmonic model ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:FREE ENERGY1.PNG|400px|thumb|left|Fig.2: Helmholtz free energy vs. temperature ]]&lt;br /&gt;
||[[File:LATTICE CONSTANT 1.PNG|400px|thumb|left|Fig.3: Lattice Constant vs. temperature ]]&lt;br /&gt;
||[[File:Cell volume.PNG|400px|thumb|left|Fig.4: Cell Volume vs. temperature ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
From fig ,it can be seen that the free energy decreases with increasing temperature. This can be explained by equation3. As temperature increases, the entropy which represents the degree of disorder also increases. This makes the TS term more positive, therefore makes the free energy more negative. From fig  and fig , the lattice constant and the cell volume increase with increasing temperature. As temperature increases, the kinetic energy of the phonons also increases, thus the crystal lattice vibrate at larger amplitude, which causes an increase in the potential energy. The equilibrium distance shifts to larger value as the repulsion force at short distance is greater than the attraction force at longer distance, which leads to the increase lattice vibrations. Therefore, thermal expansion happens. Therefore, the cell volume and the lattice parameter increase. However, in a diatomic molecule with exactly harmonic potential, the interatomic distance does not change with temperature, thus there is no thermal expansion.&lt;br /&gt;
&lt;br /&gt;
All three curves seem to be parabolic. From 300K to 1000K in the graph of the cell volume against temperature, the linear relationship follows the Quasi-harmonic approximation. From fig , the gradient of the straight line, &amp;lt;math&amp;gt;\frac{\delta V}{\delta T}&amp;lt;/math&amp;gt;, is 0.0004. Therefore by dividing the gradient by the initial volume which is 18.8365 Å³, the thermal expansion coefficient is 2.124&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics===&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; style=&amp;quot;text-align: center&lt;br /&gt;
|[[File:Cell volume vs T.PNG|450px|thumb|left|Fig.5: Cell Volume vs. temperature calculated by MD ]]&lt;br /&gt;
||[[File:Comparison1.PNG|450px|thumb|left|Fig.6: Cell Volume vs Temperature calculated by MD and quasi-harmonic approximation ]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
==Conclusion==&lt;br /&gt;
==Reference==&lt;/div&gt;</summary>
		<author><name>Xl9814</name></author>
	</entry>
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