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		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518708</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518708"/>
		<updated>2015-12-04T23:57:48Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position,&amp;lt;sup&amp;gt;4&amp;lt;/sup&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table.&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2*10&amp;lt;sup&amp;gt;-7&amp;lt;/sup&amp;gt;x&amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt; + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4*10&amp;lt;sup&amp;gt;-7&amp;lt;/sup&amp;gt;x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T) unit:K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518706</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518706"/>
		<updated>2015-12-04T23:54:25Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position,&amp;lt;sup&amp;gt;4&amp;lt;/sup&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table.&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518705</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518705"/>
		<updated>2015-12-04T23:53:58Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position,&amp;lt;sup&amp;gt;4&amp;lt;/sup&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518704</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518704"/>
		<updated>2015-12-04T23:52:20Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518703</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518703"/>
		<updated>2015-12-04T23:51:39Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518702</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518702"/>
		<updated>2015-12-04T23:51:02Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]&amp;lt;sup&amp;gt;1&amp;lt;/sup&amp;gt;]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518701</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518701"/>
		<updated>2015-12-04T23:49:27Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.1) listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518700</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518700"/>
		<updated>2015-12-04T23:47:40Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518699</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518699"/>
		<updated>2015-12-04T23:47:21Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518698</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518698"/>
		<updated>2015-12-04T23:47:03Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. &lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig.2 &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt;and can be exported back to the real space by Fourier transform. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig.1 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|fig.1 Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|fig.2 Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518696</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518696"/>
		<updated>2015-12-04T23:44:53Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. &amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518695</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518695"/>
		<updated>2015-12-04T23:43:35Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. &amp;lt;sup&amp;gt;2&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518694</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518694"/>
		<updated>2015-12-04T23:41:34Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
In the QHA primitive cell (one MgO) was used while in the molecular dynamics simulation a cell of 32 MgO was used. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
However, both method should be used in larger system in order to get more accurate results.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518692</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518692"/>
		<updated>2015-12-04T23:36:08Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics in higher temperature, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
due to the fundamental limitation of QHA the poor match to the potential distance profile, while in molecular dynamics the lattice constant can always increase.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518691</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518691"/>
		<updated>2015-12-04T23:32:42Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
In the analysis of the thermal behavior under increasing temperature, Quasi harmonic provide a relatively poor explanation than molecular dynamics. &lt;br /&gt;
There is fundamental limitation of QHA which can be shown from the shape of potential distance curve, while in molecular dynamics the lattice constant and always increase.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518690</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518690"/>
		<updated>2015-12-04T23:27:32Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
formula for calculating thermal expansion coefficient:&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518689</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518689"/>
		<updated>2015-12-04T23:26:27Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
It is clear seen that there is a steep increase of the volume around 3000K, corresponding to the phase change of the solid.&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518688</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518688"/>
		<updated>2015-12-04T23:23:25Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* quasi harmonic approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518687</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518687"/>
		<updated>2015-12-04T23:22:39Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* quasi harmonic approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
![[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
![[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518686</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518686"/>
		<updated>2015-12-04T23:21:59Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* quasi harmonic approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 &lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|centre|Brillouin zone]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518683</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518683"/>
		<updated>2015-12-04T23:20:51Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* quasi harmonic approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50 with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518681</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518681"/>
		<updated>2015-12-04T23:20:06Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* Result and discussion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518680</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518680"/>
		<updated>2015-12-04T23:19:19Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* quasi harmonic approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|DOS 1x1x1]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518679</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518679"/>
		<updated>2015-12-04T23:18:56Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518678</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518678"/>
		<updated>2015-12-04T23:17:38Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]][[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518676</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518676"/>
		<updated>2015-12-04T23:15:03Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK in brillouin zone as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
In the QHA only introduces small amount of anharmonicity, and phonon interaction is simplified and neglect. &lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518674</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518674"/>
		<updated>2015-12-04T23:07:53Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised to get the most stable geometry under different shrinking factors as shown in table ****************xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518673</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518673"/>
		<updated>2015-12-04T23:06:58Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
with coordinations W(0.5,0.25,0.75) L(0.5,0.5,0.5) G(0,0,0) X(0.5,0,0.5) W(0.5,0.25,0.75) K(0.375,0.375, 0.75) respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point (point L in the fig.xxxx) listed in phonon dispersion log file.          *******fig.&lt;br /&gt;
&lt;br /&gt;
What is more,the frequencies of degenerated vibrations 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient where x is the corresponding temperature.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518667</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518667"/>
		<updated>2015-12-04T22:57:31Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
α&amp;lt;sub&amp;gt;v&amp;lt;/sub&amp;gt;=1/V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;(∂V/∂T)&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518655</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518655"/>
		<updated>2015-12-04T22:49:56Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* Reference */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;br /&gt;
:4. K.Ishikawa, Phy. Stat. Sol., 1967, 21, 137-144&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518652</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518652"/>
		<updated>2015-12-04T22:48:23Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* Reference */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
:1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
:2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
:3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518651</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518651"/>
		<updated>2015-12-04T22:48:02Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* Reference */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;br /&gt;
1. G. K. White and O. L. Anderson, J. Applied Phys., 1966, 37, 430-432.&lt;br /&gt;
2. R. Hoffmann, Angewandte Chemie Int. Edition in Engl., 26, 846-878&lt;br /&gt;
3. O. Madelung, U. Rössler, M. Schulz (ed.), Landolt-Börnstein - Group III Condensed Matter, 1999, 41B.&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518616</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518616"/>
		<updated>2015-12-04T22:16:53Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: /* Introduction  */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|right|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation.&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518614</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518614"/>
		<updated>2015-12-04T22:16:20Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
Where WLGXWK are the points () respectively.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518612</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518612"/>
		<updated>2015-12-04T22:12:03Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble is introduced as a approximation of a system which is a&lt;br /&gt;
collection of the configurations of the system.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518608</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518608"/>
		<updated>2015-12-04T22:09:28Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 sampled along conventional pathway WLGXWK as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518604</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518604"/>
		<updated>2015-12-04T22:08:10Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in k&amp;lt;sub&amp;gt;x&amp;lt;/sub&amp;gt; k&amp;lt;sub&amp;gt;y&amp;lt;/sub&amp;gt; and k&amp;lt;sub&amp;gt;z&amp;lt;/sub&amp;gt; direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518597</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518597"/>
		<updated>2015-12-04T22:05:34Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space in kx ky and kz direction, as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept of quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518593</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518593"/>
		<updated>2015-12-04T22:03:42Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518592</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518592"/>
		<updated>2015-12-04T22:03:23Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Vibrations can be treated as particles or wave.&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518591</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518591"/>
		<updated>2015-12-04T22:02:01Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518590</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518590"/>
		<updated>2015-12-04T22:00:27Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518589</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518589"/>
		<updated>2015-12-04T21:59:55Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518588</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518588"/>
		<updated>2015-12-04T21:59:11Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518587</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518587"/>
		<updated>2015-12-04T21:58:47Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518586</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518586"/>
		<updated>2015-12-04T21:57:33Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represents a vibration model called phonon, a concept in quantum mechanics, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation using classic Newton&#039;s law. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and by the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
The higher the shrinking factor the more the k point will be selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough for the convenience in calculation. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518583</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518583"/>
		<updated>2015-12-04T21:51:15Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represent a vibration model called phonon, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
It also causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
Additionally, when k = 0 all atoms move in phase to give an infinite large wavelength. &lt;br /&gt;
&lt;br /&gt;
Molecular dynamic is a computer simulation. Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
Shrinking factor 2x2 cuts the cell into 4 pieces at the sides respectively, and the same principle apply to nxnxn in 3 dimensional space. &lt;br /&gt;
The higher the shrinking factor the more the k point selected and the more close to what happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough to calculate. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518576</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518576"/>
		<updated>2015-12-04T21:43:56Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space as shown in fig. xxx and can be exported back to the real space by Fourier transform. ****************cite fig.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represent a vibration model called phonon, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, it causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular&lt;br /&gt;
dynamic a computer simulation.&lt;br /&gt;
&lt;br /&gt;
Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
The higher&lt;br /&gt;
the shrinking factor the more the k point selected and the more close to what&lt;br /&gt;
happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough to calculate. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518573</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518573"/>
		<updated>2015-12-04T21:42:23Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space and then export back to the real space by Fourier transform.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Every k vector represent a vibration model called phonon, and it is assumed that they are independent of each other.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Additionally, it causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular&lt;br /&gt;
dynamic a computer simulation.&lt;br /&gt;
&lt;br /&gt;
Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
The higher&lt;br /&gt;
the shrinking factor the more the k point selected and the more close to what&lt;br /&gt;
happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough to calculate. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518572</id>
		<title>Rep:Mod:joannechen</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:joannechen&amp;diff=518572"/>
		<updated>2015-12-04T21:41:58Z</updated>

		<summary type="html">&lt;p&gt;Yc8712: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=== &#039;&#039;&#039;Abstract&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Computational&lt;br /&gt;
experiment was taken out to study the thermal expansion of MgO using DLVisualize and rationalised by Quasi Harmonic Approximation(QHA) and Molecular Dynamics(MD).&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Introduction &#039;&#039;&#039; ===&lt;br /&gt;
Magnesium oxide exist as face-centre cubic structure which is the analogue of NaCl, containing 4 Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; and 4 O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;  in a conventional cell.  &lt;br /&gt;
&lt;br /&gt;
Quasi&lt;br /&gt;
harmonic allows anharmonicity in some extent which equilibrium bond distance is changeable and harmonic holds for every lattice position, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
observations and calculations can be made to probe the properties of the crystal with&lt;br /&gt;
a changing volume. ************fig.&lt;br /&gt;
&lt;br /&gt;
Similar to the hypothetical hydrogen long chain the energy levels of the MgO lattice with repeated cells are contracted into energy band. ***********cite&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Calculation can be made in reciprocal space and then export back to the real space by Fourier transform.&lt;br /&gt;
Every k vector represent a vibration model called phonon, and it is assumed that they are independent of each other.&lt;br /&gt;
Numerically k equals 2 pi divided by the lattice constant &#039;a&#039; in real space, which means if the the lattice constant becomes &#039;2a&#039;, k in the reciprocal space will be haled.&lt;br /&gt;
Additionally, it causes the folding of energy against k graph. Since Mg and O are two different atoms, there will be energy gap for the branches. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Molecular&lt;br /&gt;
dynamic a computer simulation.&lt;br /&gt;
&lt;br /&gt;
Force is&lt;br /&gt;
applied to the system and the atoms are given motion, after the energy spreads&lt;br /&gt;
out the motion and other properties like temperature of the system reach an&lt;br /&gt;
equilibrium state with small fluctuation. &lt;br /&gt;
&lt;br /&gt;
The higher&lt;br /&gt;
the shrinking factor the more the k point selected and the more close to what&lt;br /&gt;
happen in the system.&lt;br /&gt;
&lt;br /&gt;
Sum of all k&lt;br /&gt;
point can represent the properties of the system, but it will take a infinite&lt;br /&gt;
time to run a calculation for infinite atoms therefor ensemble which is a&lt;br /&gt;
collection of the configurations of a system is introduced in both methods.  &lt;br /&gt;
&lt;br /&gt;
Appropriate&lt;br /&gt;
shrinking factor should be chosen which is large enough to approximate the&lt;br /&gt;
system and small enough to calculate. &lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Result and discussion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
====  quasi harmonic approximation ====&lt;br /&gt;
Phonon dispersion graph was obtained with N points = 50 as shown in fig. Dispersion N=50&lt;br /&gt;
[[File:Dispersion n=50 .jpg|300px|x300px|thumb|left|Dispersion n=50]]&lt;br /&gt;
&lt;br /&gt;
[[File:Reciprocal.JPG|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Density of states graphs were obtained with 8 different shrinking factors as shown below.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! [[File:DOS 1x1x1.jpg|300px|x300px|thumb|left|DOS 1x1x1]]&lt;br /&gt;
! [[File:DOS 2x2x2.jpg|300px|x300px|thumb|left|DOS 2x2x2]]&lt;br /&gt;
! [[File:DOS 4x4x4.jpg|300px|x300px|thumb|left|DOS 4x4x4]]&lt;br /&gt;
! [[File:DOS 6x6x6.jpg|300px|x300px|thumb|left|DOS 6x6x6]]&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| [[File:DOS 8x8x8.jpg|300px|x300px|thumb|left|DOS 8x8x8]]&lt;br /&gt;
| [[File:DOS 16x16x16.jpg|300px|x300px|thumb|left|DOS 16x16x16]]&lt;br /&gt;
| [[File:DOS 32x32x32.jpg|300px|x300px|thumb|left|DOS 32x32x32]]&lt;br /&gt;
| [[File:64x64x64.jpg|300px|x300px|thumb|left|DOS 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The shapes of the DOS change considerably over the first few graphs with the shrinking factors going from 1 to 6, the peaks spread out.&lt;br /&gt;
&lt;br /&gt;
While after 16x16x16 the fluctuations become small, giving smooth curves and a board peak. &lt;br /&gt;
&lt;br /&gt;
4 and 7 distinct peaks are clearly shown for shrinking factor 1 and 2  respectively. &lt;br /&gt;
&lt;br /&gt;
The maximum peak in each DOS are always near 400 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
It is noticeable that 64x64x64 took minutes to run, and it only contains minor difference to the 32x32x32 one.&lt;br /&gt;
&lt;br /&gt;
16x16x16 should give an good approximation of the system and it is a balance point between accuracy and calculation time.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Relationship between 1x1x1 DOS and the phonon dispersion:&lt;br /&gt;
&lt;br /&gt;
It is noticed that the K point of 1x1x1 DOS is 0.5 0.5 0.5 with corresponding frequencies: 288.49 288.49 351.76 351.76 676.23 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;,&lt;br /&gt;
&lt;br /&gt;
which is the same k vector and frequency as the 10th K point listed in phonon dispersion log file.&lt;br /&gt;
&lt;br /&gt;
What is more, with repeated frequencies 288.49 and 351.76 the densities are double those of 676.23 and 818.82 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Finding reasonable shrinking factor for the expansion part.&lt;br /&gt;
&lt;br /&gt;
Free energies were optimised under different shrinking factors as shown in table xxx&lt;br /&gt;
&lt;br /&gt;
 {| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
 ! shrinking factor&lt;br /&gt;
 ! free energy / eV&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 1x1x1&lt;br /&gt;
 | -40.930301&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 2x2x2&lt;br /&gt;
 | -40.926609&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 3x3x3&lt;br /&gt;
 | -40.926432&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 4x4x4&lt;br /&gt;
 | -40.926450&lt;br /&gt;
  &lt;br /&gt;
 |-&lt;br /&gt;
 | 5x5x5&lt;br /&gt;
 | -40.926463&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 6x6x6&lt;br /&gt;
 | -40.926471&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 7x7x7&lt;br /&gt;
 | -40.926475&lt;br /&gt;
 &lt;br /&gt;
 |-&lt;br /&gt;
 | 8x8x8&lt;br /&gt;
 | -40.926478&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 9x9x9&lt;br /&gt;
 | -40.926479&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 10x10x10&lt;br /&gt;
 | -40.926480&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 11x11x11&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 12x12x12&lt;br /&gt;
 | -40.926481&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 13x13x13&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 14x14x14&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 15x15x15&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 16x16x16&lt;br /&gt;
 | -40.926482&lt;br /&gt;
&lt;br /&gt;
 |-&lt;br /&gt;
 | 17x17x17&lt;br /&gt;
 | -40.926482&lt;br /&gt;
 &lt;br /&gt;
 |}&lt;br /&gt;
As shrinking factor increases, the change free energy converge to a finite value.  &lt;br /&gt;
&lt;br /&gt;
Shrinking factor larger than 2 with accuracy 1 meV, &lt;br /&gt;
&lt;br /&gt;
shrinking factor larger than 3 with accuracy 0.1 meV per cell.&lt;br /&gt;
&lt;br /&gt;
13 is good enough to be used as the shrinking factor in the thermal expansion .&lt;br /&gt;
&lt;br /&gt;
Free energy was optimised from 0 to 1000 Kelvin, lattice constant (volume) and free energy were recorded for analysis.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature / K&lt;br /&gt;
! Free energy / eV&lt;br /&gt;
! lattice constant / A&lt;br /&gt;
! volume / A3&lt;br /&gt;
|-&lt;br /&gt;
| 0&lt;br /&gt;
| -40.90190627&lt;br /&gt;
| 2.986563&lt;br /&gt;
| 18.836496&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| -40.90241942&lt;br /&gt;
| 2.986658&lt;br /&gt;
| 18.838268&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| -40.90937667&lt;br /&gt;
| 2.987606&lt;br /&gt;
| 18.856204&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| -40.92812366&lt;br /&gt;
| 2.989392&lt;br /&gt;
| 18.890029&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| -40.95859279&lt;br /&gt;
| 2.991633&lt;br /&gt;
| 18.932512&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| -40.99943424&lt;br /&gt;
| 2.994139&lt;br /&gt;
| 18.980117&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| -41.04931341&lt;br /&gt;
| 2.996825&lt;br /&gt;
| 19.031229&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| -41.10711691&lt;br /&gt;
| 2.999649&lt;br /&gt;
| 19.085064&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| -41.17188925&lt;br /&gt;
| 3.002595&lt;br /&gt;
| 19.141325&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| -41.24301522&lt;br /&gt;
| 3.005642&lt;br /&gt;
| 19.199648&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| -41.31984516&lt;br /&gt;
| 3.008792&lt;br /&gt;
| 19.260052&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| -41.58004206&lt;br /&gt;
| 3.018864&lt;br /&gt;
| 19.454063&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| -41.87795517&lt;br /&gt;
| 3.029987&lt;br /&gt;
| 19.669833&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| -42.20751267&lt;br /&gt;
| 3.042458&lt;br /&gt;
| 19.913641&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| -42.56474511&lt;br /&gt;
| 3.056849&lt;br /&gt;
| 20.197479&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| -42.94715413&lt;br /&gt;
| 3.074407&lt;br /&gt;
| 20.547454&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| -43.35354659&lt;br /&gt;
| 3.099267&lt;br /&gt;
| 21.049888&lt;br /&gt;
&lt;br /&gt;
|} &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin but errors were shown, &lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
possible reason is that the quasi harmonic approximation not apply at temperature too close or exceeding the melting point of a crystal.  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
PLOT Free energy against temperature. &lt;br /&gt;
[[File:Free energy.jpg|400px|x300px|thumb|left|Free energy against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
PLOT lattice constant against temperature. &lt;br /&gt;
[[File:Lattice.jpg |400px|x300px|thumb|left|Lattice constant against Temperature]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
Calculate coefficient of thermal expansion.&lt;br /&gt;
PLOT volume against temperature.&lt;br /&gt;
[[File:Volume.jpg|400px|x300px|thumb|left|Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
the trend line obtained using polynomial up to x2 for volume against temperature is: y = 2E-07x2 + 0.0002x + 18.829&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
thus dV/dT : 4E-7x + 0.0002 and it is used to calculate expansion coefficient.&lt;br /&gt;
&lt;br /&gt;
==== &amp;lt;br&amp;gt;  molecular dynamics ====&lt;br /&gt;
PLOT&lt;br /&gt;
change in volume&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Temperature&lt;br /&gt;
! Volume&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 100&lt;br /&gt;
| 599.513295&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 200&lt;br /&gt;
| 601.241595&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 300&lt;br /&gt;
| 602.899441&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 400&lt;br /&gt;
| 604.609431&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 500&lt;br /&gt;
| 606.322864&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 600&lt;br /&gt;
| 608.166535&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 700&lt;br /&gt;
| 610.085241&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 800&lt;br /&gt;
| 612.102518&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 900&lt;br /&gt;
| 614.060747&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1000&lt;br /&gt;
| 615.63532&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1300&lt;br /&gt;
| 621.914205&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1600&lt;br /&gt;
| 626.541299&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 1900&lt;br /&gt;
| 632.249813&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2200&lt;br /&gt;
| 637.052789&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2500&lt;br /&gt;
| 642.986419&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 2800&lt;br /&gt;
| 650.770808&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3100&lt;br /&gt;
| 653.844695&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| 3400&lt;br /&gt;
| 669.26276&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Attempts were made to run GULP at 3100 and 3400 kelvin and calculations were successful.&lt;br /&gt;
&lt;br /&gt;
==== Compare and comment on the difference. ====&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason volume.jpg|400px|x300px|thumb|left|volume against Temperature for both methods]]&lt;br /&gt;
&lt;br /&gt;
[[File:Comparason coefficient.jpg|400px|x300px|thumb|left|comparisons of coefficient obtained by both methods and literature value]]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;Both methods show deviations from the experimental values.&lt;br /&gt;
&lt;br /&gt;
Choosing shorter time step or larger equilibration steps and production steps may lead to a more accurate result.&lt;br /&gt;
=== &#039;&#039;&#039;Conclusion&#039;&#039;&#039; ===&lt;br /&gt;
&lt;br /&gt;
=== &#039;&#039;&#039;Reference&#039;&#039;&#039; ===&lt;/div&gt;</summary>
		<author><name>Yc8712</name></author>
	</entry>
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