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		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581185</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581185"/>
		<updated>2017-02-07T19:55:09Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has a crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
&lt;br /&gt;
The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
&lt;br /&gt;
During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model.&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking&lt;br /&gt;
factor&lt;br /&gt;
!1&lt;br /&gt;
!2&lt;br /&gt;
!3&lt;br /&gt;
!4&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|340px]]&lt;br /&gt;
|-&lt;br /&gt;
! Shrinking &lt;br /&gt;
Factor&lt;br /&gt;
!8&lt;br /&gt;
!16&lt;br /&gt;
!32&lt;br /&gt;
!64&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 1. Phonon DOS Curves at different shrinking factors.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581184</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581184"/>
		<updated>2017-02-07T19:52:32Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has a crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
&lt;br /&gt;
The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
&lt;br /&gt;
During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking&lt;br /&gt;
factor&lt;br /&gt;
!1&lt;br /&gt;
!2&lt;br /&gt;
!3&lt;br /&gt;
!4&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|340px]]&lt;br /&gt;
|-&lt;br /&gt;
! Shrinking &lt;br /&gt;
Factor&lt;br /&gt;
!8&lt;br /&gt;
!16&lt;br /&gt;
!32&lt;br /&gt;
!64&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 1. Phonon DOS Curves at different shrinking factors.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581183</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581183"/>
		<updated>2017-02-07T19:50:49Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Lattice Vibrations - Phonon Computation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
&lt;br /&gt;
The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
&lt;br /&gt;
During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking&lt;br /&gt;
factor&lt;br /&gt;
!1&lt;br /&gt;
!2&lt;br /&gt;
!3&lt;br /&gt;
!4&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|340px]]&lt;br /&gt;
|-&lt;br /&gt;
! Shrinking &lt;br /&gt;
Factor&lt;br /&gt;
!8&lt;br /&gt;
!16&lt;br /&gt;
!32&lt;br /&gt;
!64&lt;br /&gt;
|-&lt;br /&gt;
! DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 1. Phonon DOS Curves at different shrinking factors.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581182</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581182"/>
		<updated>2017-02-07T19:45:48Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Computing the Helmholtz Free Energy */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
&lt;br /&gt;
The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
&lt;br /&gt;
During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 1. Phonon DOS Curves at different shrinking factors.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581181</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581181"/>
		<updated>2017-02-07T19:44:15Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Lattice Vibrations - Phonon Computation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
&lt;br /&gt;
The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
&lt;br /&gt;
During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
|colspan = 5 | Table 1. Phonon DOS Curves at different shrinking factors.&lt;br /&gt;
|}&lt;br /&gt;
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[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581180</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581180"/>
		<updated>2017-02-07T19:38:11Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
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&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
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The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
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&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
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The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
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&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
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&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
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The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
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During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
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The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
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The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
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&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
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== Results and Discussion ==&lt;br /&gt;
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=== Quasi-Harmonic Approximation ===&lt;br /&gt;
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==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
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An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
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For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
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The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
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To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
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However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
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|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
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|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
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|}&lt;br /&gt;
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[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
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The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
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==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model (Equation 2) which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
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By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581179</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581179"/>
		<updated>2017-02-07T19:36:42Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
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The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
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The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
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&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
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The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy (A) in this model is given by Equation 2.&lt;br /&gt;
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&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
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&#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Internal energy of the lattice&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;j&#039;&#039;&#039;: Phonon bands&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&#039;&#039;&#039;: k-point in reciprocal space&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ℏ&#039;&#039;&#039;: Reduced Planck&#039;s constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;ω&#039;&#039;&#039;: Angular frequency (rad/s)&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039;: Boltzmann constant&lt;br /&gt;
&amp;lt;br&amp;gt;&#039;&#039;&#039;T&#039;&#039;&#039;: Temperature in K&lt;br /&gt;
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The second term in equation 2 represents the zero point energy and the third term gives the vibrational entropy.&lt;br /&gt;
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During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
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The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
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The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
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&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
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== Results and Discussion ==&lt;br /&gt;
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=== Quasi-Harmonic Approximation ===&lt;br /&gt;
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==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
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An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
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For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
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The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
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To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
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However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
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|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
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[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
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The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
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Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
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==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
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To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
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[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
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==== Thermal Expansion of MgO ====&lt;br /&gt;
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[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
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From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
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Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
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[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
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[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
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In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
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[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
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As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
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The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
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The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
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[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
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A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
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[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
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The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
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== Conclusion ==&lt;br /&gt;
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The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
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The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
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By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
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== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581177</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=581177"/>
		<updated>2017-02-07T19:27:12Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
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== Introduction ==&lt;br /&gt;
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[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
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The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
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The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
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The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
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\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
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The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. The Helmholtz Free Energy A in this model is given by Equation 2.&lt;br /&gt;
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&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
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During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
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The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
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The coefficient of thermal expansion is defined by Equation 3, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
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\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 3.&lt;br /&gt;
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== Results and Discussion ==&lt;br /&gt;
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=== Quasi-Harmonic Approximation ===&lt;br /&gt;
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==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
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An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
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For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
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The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
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To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
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However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
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[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
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The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
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Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
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==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
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To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
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|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
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|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
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|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
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|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
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|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
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|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
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[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
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==== Thermal Expansion of MgO ====&lt;br /&gt;
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[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
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From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
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Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
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[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
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[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
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In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
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[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
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As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
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The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
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The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:987ABC&amp;diff=581176</id>
		<title>Rep:Mod:987ABC</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:987ABC&amp;diff=581176"/>
		<updated>2017-02-07T19:26:45Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Quasi-Harmonic Approximation (QH) */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Thermal Expansion of MgO (Author: Natalie Uhlikova)   =&lt;br /&gt;
&lt;br /&gt;
[[File:MgOnice.jpeg|centre|750x300px|thumb|Picture no.1: MgO crystal: A-primitive cell, B-conventional cell (4 MgO units), C-supercell (32 MgO units)]]&lt;br /&gt;
&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
Crystals are infinite structures of atoms that repeat periodically, creating an infinite crystal lattice. Crystals unlike molecules, are described by k-space (also called &#039;&#039;reciprocal space&#039;&#039; or &#039;&#039;momentum space&#039;&#039;) with lattice parameter &#039;&#039;&#039;a*&#039;&#039;&#039; (where &amp;lt;math&amp;gt;\frac{2\pi}{a}=a*&amp;lt;/math&amp;gt;) where &#039;&#039;a&#039;&#039; is the lattice parameter in the real space. Atoms in the lattice don&#039;t vibrate independently. The collective vibrational modes of an infinite crystal lattice are called &#039;&#039;phonons&#039;&#039;&amp;lt;ref name=&amp;quot;:0&amp;quot;&amp;gt;R. Hoffman, &#039;&#039;Angewandte Chemie International Edition in English&#039;&#039;, 1987, &#039;&#039;&#039;26&#039;&#039;&#039;, 846-878&amp;lt;/ref&amp;gt;, which are equivalent to photons with respect to electronic states. Dispersion relation E(k) curve shows the energy of individual states as a function of &#039;&#039;&#039;k&#039;&#039;&#039;, the wave-vector. The first Brillouin zone lies within a range of unique k values |&#039;&#039;&#039;k&#039;&#039;&#039;| ≥ π/a, any value outside of this interval is only a repetition as the reciprocal space is periodic.The density of states (DOS) is inversely proportional to the E(k) slope.    &lt;br /&gt;
&lt;br /&gt;
The atoms in the lattice are attracted to each other by Coulombic forces. To avoid collision of anionic oxygen and cationic magnesium, the Buckingham potential (repulsive force) is employed.  &lt;br /&gt;
&lt;br /&gt;
A primitive cell of MgO takes shape of rhombohedron (picture no. 1). It is the smallest cell that can be translated in space to generate the crystal. The primitive unit cell was used for all calculations within the quasi-harmonic mode. A cubic conventional cell is easy to visualise, but not suitable for calculations in this case. Supercell will be employed into molecular dynamics calculations as it is desirable to have a larger system, so that more accurate results can be achieved.    &lt;br /&gt;
&lt;br /&gt;
Thermal energy is sum of energy of all vibrational modes present in the crystal at a given temperature. The physical origin of thermal expansion consists in the anharmonic nature of interatomic interaction potential. At higher temperatures, the atoms vibrate with higher amplitude and hence the average value of interatomic separation increases. Thermal expansion coefficient &#039;&#039;&#039;α&#039;&#039;&#039; is given by the following formula:    &lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;\alpha=\frac{1}{V_0}\left(\frac{\partial V}{\partial T}\right)_P&amp;lt;/math&amp;gt;    &lt;br /&gt;
&lt;br /&gt;
where V&amp;lt;sub&amp;gt;0 &amp;lt;/sub&amp;gt;(Å&amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt;) is the initial cell volume at 0K, V(Å&amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt;) is volume at temperature T(K). Partial derivative of volume with respect to temperature is the slope of graph of volume vs. temperature at constant pressure.     &lt;br /&gt;
&lt;br /&gt;
=== Objectives ===&lt;br /&gt;
The aim of this lab is to study thermodynamic expansion of MgO crystal by carrying out computational simulations based on two principles: 1) quasi-harmonic approximation and 2) molecular dynamics.&lt;br /&gt;
&lt;br /&gt;
== Methodology ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation (QH) ===&lt;br /&gt;
This method approaches crystal dynamics from quantum-mechanical point of view using a reciprocal space. The lattice dynamic of MgO crystal is investigated by approximating that all vibrations are of harmonic nature and can be described by a parabolic function. Helmholtz free energy per unit cell can be calculated as a function of volume and temperature. The unit cell is optimised to find energy minimum at each temperature in the range ∈ &amp;lt;0;2579&amp;gt; K. The Helmholtz free energy &#039;&#039;&#039;A&#039;&#039;&#039; is given by the following formula:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;A=E_0 + \frac{1}{2}\sum_{\mathbf{k}, i}\hbar\omega_j,_k + k_BT\sum_{\mathbf{k}, i}ln[1-exp(\frac{-\hbar\omega_j,_k}{k_BT})]&amp;lt;/math&amp;gt;&lt;br /&gt;
&lt;br /&gt;
where &#039;&#039;&#039;E&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt;&#039;&#039;&#039; is the internal lattice energy, the second term represents zero point energy and the third term stands for vibrational entropy; &#039;&#039;&#039;j&#039;&#039;&#039; represents phonon bands, &#039;&#039;&#039;k&#039;&#039;&#039; is abbreviation of k-point in the reciprocal space, &#039;&#039;&#039;ℏ&#039;&#039;&#039; is reduced Planck&#039;s constant, &#039;&#039;&#039;ω&#039;&#039;&#039; is angular frequency (rad/s), &#039;&#039;&#039;k&amp;lt;sub&amp;gt;B&amp;lt;/sub&amp;gt;&#039;&#039;&#039; is Boltzmann constant and &#039;&#039;&#039;T&#039;&#039;&#039; is temperature in K.      &lt;br /&gt;
&lt;br /&gt;
Limitations to this method: The atoms are not allowed to move, so their equilibrium bond distance does not change as a function of temperature, i. e. the positions of nuclei are fixed and thus bonds are not allowed to break in this approximation.&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics (MD) ===&lt;br /&gt;
Molecular dynamics obeys the second Newton law &#039;&#039;&#039;F=ma &#039;&#039;&#039;( where &#039;&#039;F(N)&#039;&#039; is force, &#039;&#039;m(kg)&#039;&#039; is mass and &#039;&#039;a(m/s)&#039;&#039; is acceleration) and investigates average system behaviour over a period of time. The computational simulation operates on a real space where atom positions are not fixed and hence they are allowed to move and bonds can break. The zero point energy is being ignored. Calculation was carried out on a supercell containing 32 MgO units. This number results from a compromise between having enough flexible space for atoms to move and reasonably short time for calculations. The real trajectory of atoms is simulated. The following settings was applied: A time step &#039;&#039;dt = &#039;&#039;10&amp;lt;sup&amp;gt;-15 &amp;lt;/sup&amp;gt;s, which is long enough for calculation to be efficient; 500 equilibration and production steps, 5 sampling steps and trajectory write steps.  &lt;br /&gt;
&lt;br /&gt;
Limitations to this method: The zero point energy cannot be calculated.  &lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
[[File:PhononDispersion1x1x1.jpeg|right|550x250px|thumb|Picture no. 2: Phonon dispersion graph at grid size 1x1x1]]&lt;br /&gt;
&lt;br /&gt;
=== Lattice Dynamics ===&lt;br /&gt;
Picture no. 2. shows the phonon dispersion that was computed on 50 k-point. Note that this number of k-points doesn&#039;t give the best resolution, but is it just good enough to allow for a reliable phonon dispersion calculation. In general, 6 vibrational branches are observed, occasionally less due to degenerate vibrational modes.    &lt;br /&gt;
&lt;br /&gt;
The value of k cannot be changed as it spans over the range ± π/a, but the grid size can be adjusted i.e. it can be changed how many times the E(k) reading is taken via the shrinking factor. The following empirical formula is valid for shrinking factor n&amp;gt;1: no. of k-points =&amp;lt;math&amp;gt;\frac{n^3}{2}&amp;lt;/math&amp;gt;, where n is the shrinking factor, so for example shrinking factor 2 has 4 k-points, n=4 contains 32 k-points etc...  &lt;br /&gt;
  &lt;br /&gt;
[[File:DOS1x1x1.jpeg|right|550x250px|thumb|Picture no. 3: DOS for grid size 1x1x1, calculated at a k-point (0.5,0.5,0.5) (referred as &#039;&#039;&#039;L point&#039;&#039;&#039;)]]&lt;br /&gt;
Picture no.3 shows a DOS graph for 1x1x1 grid calculated using a single k-point (0.5,0.5,0.5), which corresponds to a symmetry point L (see picture no. 2). Based on the assumption that as there are two atoms in the unit (Mg and O) in a three-dimensional space, six unique branches (vibrational bands) should be expected. There are only four peaks in the graph at the frequencies 286 and 351 Hz (0.333 intensity) and 676 and 806 Hz (0.167 intensity). The two higher intensity peaks are doubly degenerate, hence only four peaks are observed. The bigger the grid size, the better the &#039;resolution&#039; of the DOS curve and hence more accurate picture of the states. By changing the grid size gradually by a factor of 2, the DOS curve became progressively smoother. There was no noticeable difference in the shape observed when changing the shrinking factors from 32x32x32 to 64x64x64. As a consequence, the grid size 32x32x32 was established as the optimal grid size and was utilised for all further calculations to achieve high enough resolution in a reasonable time.  &lt;br /&gt;
&lt;br /&gt;
To further justify the above conclusion in a quantitative way, Helmholtz free energy was computed for various grid sizes. The smaller grid sizes displayed significant fluctuations in the free energy values, but it levelled out at -40.926483 eV once a grid size 32x32x32 was reached (picture no. 5). The most dramatic change in free energy appeared at low sampling when grid size was changed from 1x1x1 to 2x2x2. Accuracy in energy determination to 1meV can be achieved with grid 8x8x8, accuracy to 0.5 meV and 0.1 with 16x16x16 grid.    &lt;br /&gt;
&lt;br /&gt;
[[File:DOS.jpeg|right|700x400px|thumb|Picture no. 4: DOS variation with grid size (increasing from B to G); B-2x2x2, C-4x4x4, D-8x8x8, E-16x16x16, F-32x32x32, G-64x64x64]]&lt;br /&gt;
[[File:optimumgridsize.jpeg|right|600x300px|thumb|Picture no. 5: Variation of free energy with grid size; Grid type: 1: 1x1x1, 2: 2x2x2, 3: 4x4x4, 4: 8x8x8, 5: 16x16x16, 6: 32x32x32, 7: 64x64x64]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
When considering whether the 32x32x32 grid size would be suitable for performing calculations for other crystal structures, the relative size of lattice parameter &#039;&#039;a&#039;&#039; in the real space and the inverse equivalent &#039;&#039;a*&#039;&#039; in the reciprocal space should be taken into account. It is expected that for a dimensionally similar oxide CaO with a = 4.7-4.8 Å&amp;lt;ref&amp;gt;E. Albuquerque and M. Vasconcelos, &#039;&#039;Journal of Physics: Conference Series&#039;&#039;, 2008, &#039;&#039;&#039;100&#039;&#039;&#039;, 42006&amp;lt;/ref&amp;gt; the optimum grid 32x32x32 for MgO should be sufficient to obtain a convenient resolution. Zeolite is a large structure, its lattice constant &#039;&#039;a&#039;&#039; ranges between 24.2-25.1 Å&amp;lt;ref&amp;gt;J. A. Kaduk and J. Faber, &#039;&#039;The Rigaku Journal, &#039;&#039;1995, &#039;&#039;&#039;12&#039;&#039;&#039;, 14-34.&amp;lt;/ref&amp;gt; for faujasite. MgO lattice constant equals roughly 3 Å, which means that in k-space a* of MgO is bigger than a* of zeolite and thus lower grid-size would be needed for description of zeolite to achieve equally good results as for MgO. The same trend would apply to metals, but with different reasoning behind. In comparison to MgO, the sea of free electrons in metals moderate repulsion between &#039;stationary&#039; cations and hence lower the width of the band structure. i. e. metals give rise to smaller/narrower band width (and hence higher DOS) and therefore metals can be described by lower number of k-points to achieve a sufficient resolution. The optimal grid size for MgO is suitable for metal DOS simulations.&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
The two curves for MD and QH approximation display a similar linear behaviour (picture no. 6). At lower temperatures, QH line deviates noticeably from the linear fit, whereas MD curve nicely obeys the linear trend. Molecular dynamic simulation is more suitable to perform calculations operating close to the melting temperature, because the bonds are allowed to break. Melting point of MgO is around 3250 K&amp;lt;ref&amp;gt;C. Ronchi and Mikhail Sheindlin, &#039;&#039;Journal of Applied Physics&#039;&#039;, 2001, &#039;&#039;&#039;90&#039;&#039;&#039;.&amp;lt;/ref&amp;gt;. There is a small drop in the unit cell volume for MD curve at temperatures approaching the melting point (&amp;gt;2600K). Contrary to that the quasi-harmonic curve keeps increasing as atoms are not allowed to dissociate and therefore the lattice parameter increases to the infinity after passing the melting point (picture no. 8).&lt;br /&gt;
&lt;br /&gt;
[[File:QHvsMD.jpeg|right|750x350px|thumb|Picture no. 6: Thermal expansion QH and MD approach comparison ]]&lt;br /&gt;
[[File:0to1000at321.jpeg|right|600x300px|thumb|Picture no. 7: Free energy change as a function of temperature in the range 100-1000 K]]&lt;br /&gt;
[[File:latticeparam1.jpeg|right|600x500px|thumb|Picture no. 8: Thermal expansion of lattice parameter vs temperature ]]&lt;br /&gt;
&lt;br /&gt;
When using quasi-harmonic approximation, thermal expansion coefficient was found &#039;&#039;α&#039;&#039; = 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, when applying molecular dynamics &#039;&#039;α&#039;&#039; = 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. In comparison to the literature values (both calculated by QH method) 1.334x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;A. S. Madhusudhan Rad and K. Narender, &#039;&#039;Journal of Thermodynamics&#039;&#039;, 2014, 4.&amp;lt;/ref&amp;gt; (extrapolated at T range &amp;lt;300,1000&amp;gt; K) and 1.260x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;&amp;lt;ref&amp;gt;C. J. Engberg and E. H. Zehms, &#039;&#039;Journal of the American Ceramic Society&#039;&#039;, 1959, &#039;&#039;&#039;42&#039;&#039;&#039;, 304.&amp;lt;/ref&amp;gt; from range at higher temperatures &amp;lt;1000,2000&amp;gt;K, the experimental QH and MD thermal expansion coefficients are of the same magnitude but with slightly higher multiplier.   &lt;br /&gt;
&lt;br /&gt;
The size of the supercell (32 MgO units) seems therefore to create a reasonably big sample for the simulation that did not require too much processing time. A supercell structure of 64 MgO units would serve as a more accurate representation of the real crystal structure as there is more freedom of movement and large set of data to be averaged over a period of time. Based on the ease of calculation time for system of 32 units, a supercell containing 64 MgO might be useful and feasible sell size for future calculations.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==  &lt;br /&gt;
  &lt;br /&gt;
In this lab the thermal expansion of MgO crystal was simulated using two different methods: phonon-based &#039;&#039;lattice dynamics&#039;&#039; (quasi-harmonic approximation) and classical Newtonian &#039;&#039;molecular dynamics&#039;&#039;. An optimal grid size that delivered the best resolution in the most reasonable amount of time was found to have shrinking factors 32x32x32. The optimal grid and primitive unit cell was utilised to calculate Helmholtz free energy as a function of temperature in the range &amp;lt;0,2579&amp;gt; K. When using quasi-harmonic approximation, thermal expansion coefficient was found to be &#039;&#039;α&#039;&#039; = 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, when using molecular dynamics &#039;&#039;α&#039;&#039; = 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. Both values are in good agreement with literature values&amp;lt;ref name=&amp;quot;:0&amp;quot; /&amp;gt; which suggests calculations were carried out correctly with a sufficient lattice sampling. Molecular dynamic approach predicts thermal expansion better at temperatures closer to the melting point, lattice dynamics is more suitable for low temperatures calculations, particularly at 0K, where molecular dynamics fails to predict the zero point energy. &lt;br /&gt;
&lt;br /&gt;
== Reference ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Adc&amp;diff=576737</id>
		<title>Adc</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Adc&amp;diff=576737"/>
		<updated>2017-01-23T22:03:14Z</updated>

		<summary type="html">&lt;p&gt;Egn14: Blanked the page&lt;/p&gt;
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&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
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		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Adc&amp;diff=576736</id>
		<title>Adc</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Adc&amp;diff=576736"/>
		<updated>2017-01-23T22:02:23Z</updated>

		<summary type="html">&lt;p&gt;Egn14: Created page with &amp;quot;== Introduction ==  right File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primit...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576735</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576735"/>
		<updated>2017-01-23T21:56:38Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Results and Discussion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
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==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
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[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;br /&gt;
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[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
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In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
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The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
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== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
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The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
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By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
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== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576734</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576734"/>
		<updated>2017-01-23T21:54:02Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
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&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
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The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
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The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
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The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
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&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
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The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
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The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
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The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
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\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
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== Results and Discussion ==&lt;br /&gt;
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=== Quasi-Harmonic Approximation ===&lt;br /&gt;
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==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
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An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
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For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
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The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
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To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
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However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
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| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
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[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
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The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
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Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
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==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
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To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
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{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
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[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576733</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576733"/>
		<updated>2017-01-23T21:52:38Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Computing the Helmholtz Free Energy */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576732</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576732"/>
		<updated>2017-01-23T21:51:52Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Quasi-Harmonic Approximation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576731</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576731"/>
		<updated>2017-01-23T21:51:23Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576730</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576730"/>
		<updated>2017-01-23T21:50:26Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Conclusion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO. The deviations at lower temperatures were determined to be due to the consideration of the quantum mechanical zero-point energy in the quasi-harmonic approximation which was absent in the Newtonian mechanics based molecular dynamics approach. The deviations at higher temperatures were due to the oversight of the possibility for bonds to break in the quasi-harmonic model which led to continuous expansion of the crystal lattice. Molecular dynamics nonetheless took bond breakage into account and allowed for a phase change at high temperatures.&lt;br /&gt;
&lt;br /&gt;
By evaluating the limitations of each model, it can be concluded that at lower temperatures, the quasi-harmonic model is better at predicting thermal expansion whereas at higher temperatures, molecular dynamics would give the better approximation. &lt;br /&gt;
&lt;br /&gt;
== References ==&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576725</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576725"/>
		<updated>2017-01-23T21:34:47Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Conclusion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approaches in this experiment. The appropriate shrinking factor was determined to be 32 for the quasi-harmonic model. This was done by generating DOS curves for several shrinking factors and weighing the degree of resolution against computational cost. A further justification of this grid size was made by observing the degree of convergence in the Helmholtz free energy values as the shrinking factor increased. In contrast, the appropriate grid size for molecular dynamics calculations was not empirically established due to the its greater computational cost.&lt;br /&gt;
&lt;br /&gt;
The calculated Helmholtz free energy was observed to decrease as a function of temperature. This can be rationalised by a greater entropic contribution at higher temperatures. The lattice parameters and cell volume were then calculated as a function of temperature with both models. The deviations in cell volume values between each model occurred at lower temperatures (100-500 K) and at higher temperatures close to the melting point of MgO.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576721</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576721"/>
		<updated>2017-01-23T21:15:21Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Results and Discussion */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
&lt;br /&gt;
==== Lattice Vibrations - Phonon Computation ====&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approach in this experiment.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576720</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576720"/>
		<updated>2017-01-23T21:13:26Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;br /&gt;
&lt;br /&gt;
== Conclusion ==&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of the MgO crystal lattice was simulated using the quasi-harmonic and molecular dynamics approach in this experiment.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576717</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576717"/>
		<updated>2017-01-23T21:08:16Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure (Plot 4.), the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576716</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576716"/>
		<updated>2017-01-23T21:05:59Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576714</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576714"/>
		<updated>2017-01-23T21:03:06Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be 3.185x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; for the molecular dynamics model. This value is in better agreement with the literature value as compared to the value obtained from the quasi-harmonic model.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576713</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576713"/>
		<updated>2017-01-23T20:56:38Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.|none]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VOL TEMP egn14.png|thumb|400x400px|Plot 7. Plot of cell volume as a function of temperature (molecular dynamics).|none]]&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient was calculated to be&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_VOL_TEMP_egn14.png&amp;diff=576711</id>
		<title>File:MD VOL TEMP egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_VOL_TEMP_egn14.png&amp;diff=576711"/>
		<updated>2017-01-23T20:51:02Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576710</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576710"/>
		<updated>2017-01-23T20:49:53Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt;and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576708</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576708"/>
		<updated>2017-01-23T20:47:33Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;br /&gt;
&lt;br /&gt;
[[File:MD EXTRAVolTemp egn14.png|thumb|400x400px|Plot 6. Plot of cell volume as a function of temperature (100-2500 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
A comparison between both models at higher temperatures can be drawn from plot 6. At higher temperatures approaching the melting point of MgO at 3125 K, the Mg&amp;lt;sup&amp;gt;2+ &amp;lt;sup/&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;sup/&amp;gt; bonds break as a solid to molten phase change occurs. This behaviour is not accounted for within the quasi-harmonic model as it does not allow for the bonds to break and instead gives rise to continuous expansion of the crystal lattice. The molecular dynamics model allows bond breakage for a phase change to occur, and is thus the more accurate model at higher temperatures.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_EXTRAVolTemp_egn14.png&amp;diff=576706</id>
		<title>File:MD EXTRAVolTemp egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_EXTRAVolTemp_egn14.png&amp;diff=576706"/>
		<updated>2017-01-23T20:31:39Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576704</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576704"/>
		<updated>2017-01-23T20:29:47Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;br /&gt;
&lt;br /&gt;
The smaller cell volume values from the molecular dynamics approach relative to the quasi-harmonic model at lower temperatures is due to the consideration of the zero-point energy within the equation for the Helmholtz free energy in the quasi-harmonic model which is in turn used in determining the cell volume. The zero-point energy is a product of the quantum mechanical Heisenberg uncertainty principle and therefore its consideration is absent within the classical mechanics based molecular dynamics model.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576701</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576701"/>
		<updated>2017-01-23T20:19:00Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;br /&gt;
&lt;br /&gt;
[[File:MD VolTemp egn14.png|thumb|400x400px|Plot 5. Plot of cell volume as a function of temperature (100-1000 K) for quasi-harmonic and molecular dynamics simulations.]]&lt;br /&gt;
&lt;br /&gt;
As can be seen in Plot 5, there is an upward trend in cell volume as a function of temperature for both the quasi-harmonic and molecular dynamics models. At lower temperatures, the molecular dynamics approach gave significantly smaller cell volumes than the quasi-harmonic model but the values converge at higher temperatures but are not identical. &lt;br /&gt;
&lt;br /&gt;
The upward trend can be explained by an increase in thermal energy within the system due to elevated temperatures causing an increased accessibility to higher energy vibrational modes. A greater repulsion between nuclei occur at these higher energy vibrational states giving rise to elongated bond lengths and thus larger cell volumes.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_VolTemp_egn14.png&amp;diff=576699</id>
		<title>File:MD VolTemp egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MD_VolTemp_egn14.png&amp;diff=576699"/>
		<updated>2017-01-23T20:01:37Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576698</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576698"/>
		<updated>2017-01-23T19:57:27Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Supercell32 egn14.png|thumb|300x300px|Image 4. Supercell containing 32 MgO units]]&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units (Image 4.) is used for the molecular dynamics calculations.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Supercell32_egn14.png&amp;diff=576697</id>
		<title>File:MgO Supercell32 egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Supercell32_egn14.png&amp;diff=576697"/>
		<updated>2017-01-23T19:56:14Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576696</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576696"/>
		<updated>2017-01-23T19:54:38Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Plot 2. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Plot 3. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From Plot 3 and Plot 4, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in Plot 2. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Plot 4. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units is used for the molecular dynamics calculations.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576695</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576695"/>
		<updated>2017-01-23T19:52:59Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Computing the Helmholtz Free Energy */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Plot 1. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units is used for the molecular dynamics calculations.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576694</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576694"/>
		<updated>2017-01-23T19:51:34Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Molecular Dynamics */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;br /&gt;
&lt;br /&gt;
In the molecular dynamics method, the free motion of atoms means that a larger number of cells is essential to provide vibrational flexibility and more accurately simulate the different vibrational modes of the MgO crystal lattice. Hence, a supercell containing 32 MgO units is used for the molecular dynamics calculations.&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576691</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576691"/>
		<updated>2017-01-23T19:10:13Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; using Equation 2. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576690</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576690"/>
		<updated>2017-01-23T19:09:02Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined by Equation 2, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 2.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576689</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576689"/>
		<updated>2017-01-23T19:06:33Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576688</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576688"/>
		<updated>2017-01-23T19:05:59Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576687</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576687"/>
		<updated>2017-01-23T19:05:16Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice. The atomic velocities and configurations are then updated at regular time intervals or steps and the lattice parameters and cell volume recorded. A sufficiently large time step is used to minimise the effect of fluctuations so that a reliable average value for physical properties such as temperature and energy is obtained.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576686</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576686"/>
		<updated>2017-01-23T18:58:43Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The thermal expansion of MgO will be monitored by two different computational methods. The first of which is the quasi-harmonic model which models the crystal vibrations as a harmonic oscillator. During thermal expansion, the Helmholtz free energy is minimised at each temperature which leads to a shift in the parabolic potential. This means that the equilibrium bond length is shifted at each temperature giving rise to thermal expansion of the crystal lattice. A repulsive term is also included in this model to ac&lt;br /&gt;
&lt;br /&gt;
The second method is molecular dynamics which relies on classical mechanics. In this model, the motions of individual atoms are unrestricted and obey Newton&#039;s second law. Initial velocities dependent on temperature are assigned to each atom within the crystal while the initial configuration of atoms follows that of the ideal MgO lattice.    the in  according to their  assigned velocities which are dependent on the temperature. The lattice parameters and cell volume are then recorded at regular time intervals or steps&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576683</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576683"/>
		<updated>2017-01-23T18:00:04Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal. The phonon dispersion relation for a 1D chain of atoms which relates the vibrational frequency to the k-values is shown in equation 1. where ω&amp;lt;sub&amp;gt;k &amp;lt;/sub&amp;gt; represents the frequency of vibration and M is the mass of atoms.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\omega_k = \sqrt{\frac{4J}{M}}\left|sin\left(\frac{ka}{2}\right)\right|&lt;br /&gt;
&amp;lt;/math&amp;gt; -- Equation 1.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576682</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576682"/>
		<updated>2017-01-23T17:52:39Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values. The propagation of vibrations within the crystal can be visualised by monitoring the variation in phonon frequencies at different k-points. A phonon dispersion as a function of k-values can then be generated that describes the vibrational states within the crystal.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576678</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576678"/>
		<updated>2017-01-23T17:25:42Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
The periodicity of the MgO crystal lattice means that it can be represented by a translational vector in real space. Similarly, a fourier transformation would allow a description of the MgO lattice in reciprocal space where various physical properties can be described by the wave vectors or k-values.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576669</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576669"/>
		<updated>2017-01-23T17:09:33Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Conventionalcell egn14.png|thumb|300px|Image 1. Conventional cell of MgO.|right]]&lt;br /&gt;
[[File:MgO Primitivecell egn14.png|thumb|300px|Image 2. Primitive cell of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt;2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt;2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Primitivecell_egn14.png&amp;diff=576668</id>
		<title>File:MgO Primitivecell egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Primitivecell_egn14.png&amp;diff=576668"/>
		<updated>2017-01-23T17:08:17Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Conventionalcell_egn14.png&amp;diff=576667</id>
		<title>File:MgO Conventionalcell egn14.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Conventionalcell_egn14.png&amp;diff=576667"/>
		<updated>2017-01-23T17:07:15Z</updated>

		<summary type="html">&lt;p&gt;Egn14: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576664</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576664"/>
		<updated>2017-01-23T17:03:00Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Lattice Vibrations - Phonon Computation */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt; 2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt; 2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 3. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
&lt;br /&gt;
From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
&lt;br /&gt;
The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
&lt;br /&gt;
Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
&lt;br /&gt;
=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576663</id>
		<title>Rep:MgO egn14</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:MgO_egn14&amp;diff=576663"/>
		<updated>2017-01-23T17:01:51Z</updated>

		<summary type="html">&lt;p&gt;Egn14: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
== Introduction ==&lt;br /&gt;
&lt;br /&gt;
The aim of this computational experiment is to simulate the thermal expansion of a magnesium oxide (MgO) crystal lattice using different models, and in the process calculate the coefficient for thermal expansion. &lt;br /&gt;
&lt;br /&gt;
The system under investigation is MgO in the solid state. In this state, MgO has crystalline structure where there is long-range order. This means that if the relative positions of an atom and its neighbours are known at a particular point, it is then possible to pin-point the positions of these atoms throughout the crystal by virtue of the periodic structure. Hence, solid MgO can be represented by a unit cell - a basic building block that is repeated periodically to generate the entire crystal lattice. The conventional unit cell of MgO is the &#039;NaCl unit cell&#039; (Image 1.) which can be viewed as a simple face-centred cubic (FCC) cell where the Mg atoms occupy the octahedral holes of the oxygen&#039;s sub-lattice and the oxygen atoms occupy the octahedral holes of the magnesium sub-lattice. Another way of viewing this unit cell is as two interpenetrating FCC cells of Mg and O displaced from each by half of the body-diagonal. A less common representation of the MgO lattice is by using its rhombohedron primitive cell (Image 2.). In either case, the crystal lattice is held together by strong ionic interactions between the oppositely charged Mg&amp;lt;sup&amp;gt; 2+ &amp;lt;/sup&amp;gt; and O&amp;lt;sup&amp;gt; 2- &amp;lt;/sup&amp;gt; ions.&lt;br /&gt;
&lt;br /&gt;
== Results and Discussion ==&lt;br /&gt;
&lt;br /&gt;
=== Lattice Vibrations - Phonon Computation ===&lt;br /&gt;
&lt;br /&gt;
An appropriate grid size of the MgO crystal had to be determined prior to performing computations in the quasi-harmonic approximation. The grid size is represented by shrinking factors along each direction of the crystal. This was done by examining phonon Density of States (DOS) graphs as a function of shrinking factor. The number of k-points included in the DOS computation varies as a function of shrinking factor. &lt;br /&gt;
&lt;br /&gt;
For the shrinking factor of 1, i.e a lattice of grid size 1x1x1, one k-point which was 0.5 multiplied by the lattice vector in each direction of the crystal was included. This k-point (0.5, 0.5, 0.5) corresponds to the symmetry point L.&lt;br /&gt;
&lt;br /&gt;
The density of states graphs were plotted for the shrinking factors 1, 2, 3, 4, 8, 16, 32 and 64. It was observed that larger shrinking factors gave smoother DOS curves of higher resolution. This is due to the fact that a larger shrinking factor corresponds to a smaller Brillouin zone. This means that a greater number of k-points is used in the computations and more phonon frequencies are included.&lt;br /&gt;
&lt;br /&gt;
To determine an appropriate grid size for a reasonable DOS approximation, a sufficiently well-resolved DOS curve had to be observed. From observing the DOS curves in table 1, a shrinking factor of 16 was determined to be the minimum grid size which produced a reasonable DOS curve. The 16x16x16 DOS curve was determined to be reasonable by comparing its appearance to those of smaller and larger shrinking factors. There was a significant change in the DOS curve appearance going from the 8x8x8 grid to the 16x16x16 grid but only a minor improvement in resolution going to the larger grid sizes of 32x32x32 and 64x64x64. Therefore, if computational power or time was extremely limited, performing computations using a shrinking factor of 16 would suffice.&lt;br /&gt;
&lt;br /&gt;
However, the optimal grid size for the proceeding computations in the quasi-harmonic model was determined to be that with a shrinking factor of 32. This is because the shrinking factor of 32 gave a more detailed DOS curve than the shrinking factor of 16, and both calculations took roughly the same amount of time to complete. A shrinking factor of 64 was not chosen because the minor improvement in resolution in the DOS curve was greatly offset by the significantly longer computational time and was determined to be inordinately computationally costly.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
! Shrinking factor&lt;br /&gt;
! 1&lt;br /&gt;
! 2&lt;br /&gt;
! 3&lt;br /&gt;
! 4&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS 1x1x1.png|350px]]&lt;br /&gt;
| [[File:DOS2x2x2.png|350px]]&lt;br /&gt;
| [[File:DOS3x3x3.png|350px]]&lt;br /&gt;
| [[File:DOS4x4x4.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
| Shrinking Factor&lt;br /&gt;
| 8&lt;br /&gt;
| 16&lt;br /&gt;
| 32&lt;br /&gt;
| 64&lt;br /&gt;
|-&lt;br /&gt;
| DOS Curve&lt;br /&gt;
| [[File:DOS8x8x8.png|350px]]&lt;br /&gt;
| [[File:DOS16x16x16.png|350px]]&lt;br /&gt;
| [[File:DOS32x32x32.png|350px]]&lt;br /&gt;
| [[File:DOS64x64x64.png|350px]]&lt;br /&gt;
|-&lt;br /&gt;
&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Dispersiondiagramegn14.png|thumb|400px|Image 1. Phonon dispersion of MgO.|right]]&lt;br /&gt;
&lt;br /&gt;
The dispersion curve is an alternative representation of the lattice vibrational states and their energies. The variation of the energies of vibrations with respect to different k-points is illustrated in a dispersion curve. Symmetry points are k-points of extra importance and are highlighted in the dispersion curve. Information such as the energies and number of vibrational states at different k-points within the crystal can be extracted from the dispersion curve. This is in contrast to the DOS curves which show the proportion of &lt;br /&gt;
vibrational states at a given energy interval based on the number of k-points provided which is governed by the grid size.&lt;br /&gt;
&lt;br /&gt;
Based on the optimal grid size with shrinking factor of 32 for the MgO lattice, several assumptions on the optimal grid sizes for other species can be made by considering their lattice sizes relative to that of MgO. Namely, lattices with similar lattice parameter (a) and inverse lattice parameter (b) magnitudes would be expected to share a common optimal grid size with the MgO lattice. The lattice parameter (a) of MgO is 4.2 Å&amp;lt;ref&amp;gt;http://www.crystec.de/daten/mgo.pdf&amp;lt;/ref&amp;gt;. Firstly, for a similar oxide such as CaO (a = 4.7 - 4.8 Å&amp;lt;ref&amp;gt;1.II-VI and I-VII Compounds; Semimagnetic Compounds, 1999, 1-3.&amp;lt;/ref&amp;gt; with a primitive cell of similar dimensions to MgO, the inverse lattice parameter would be similar, hence the Brillouin zone would be similar in size, which means that the same number of k-points would be needed to generate a DOS curve of sufficient resolution. This means that the same shrinking factor of 32 would be adequate for CaO. &lt;br /&gt;
Zeolites generally have larger structures with larger primitive cells. For instance, Faujasite has a lattice parameter around 24.6Å&amp;lt;ref&amp;gt; D. N. Stamires, Clays and Clay Minerals, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, 379-389&amp;lt;/ref&amp;gt; which is significantly larger than MgO. This means that the cells in reciprocal space of Zeolites are significantly smaller than MgO. Hence, a smaller shrinking factor than 32 which corresponds to fewer sampled k-points would likely be adequate for a well-resolved DOS curve.&lt;br /&gt;
A smaller number of k-points from a smaller shrinking factor than 32 would also suffice for a regular metal lattice like Li. This is due to the higher DOS or narrower band widths characteristic of regular metal lattices. This narrower band width can be attributed to the cushioning of the repelling positive cations undergoing vibrational motion by the sea of electrons surrounding the cations. As a consequence, there is minimal fluctuation in the vibrational energy levels.&lt;br /&gt;
&lt;br /&gt;
=== Quasi-Harmonic Approximation ===&lt;br /&gt;
==== Computing the Helmholtz Free Energy ====&lt;br /&gt;
&lt;br /&gt;
To further justify the choice of grid size with shrinking factor 32, calculations of the Helmholtz free energies as a function of grid size was performed. As the grid sizes increased, the Helmholtz free energy converged to a greater extent towards the value of the infinite grid. This is evident in the decreasing degree of fluctuation with grid size. i.e a smaller change in Helmholtz free energy values was observed for the larger grid sizes. There was no change in Helmholtz free energy value going from shrinking factor 32 to 64, which indicates complete convergence. A shrinking factor of 2 results in a free energy value accurate to 1 meV and 0.5 meV, and a shrinking factor of 4 gives a free energy value accurate to 0.1 meV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
!Shrinking Factor&lt;br /&gt;
!Helmholtz Free Energy (eV)&lt;br /&gt;
!Change in Energy&lt;br /&gt;
|-&lt;br /&gt;
|1&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9303&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|&lt;br /&gt;
|-&lt;br /&gt;
|2&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9266&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|3.69x10&amp;lt;sup&amp;gt;-3&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|4&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.59x10&amp;lt;sup&amp;gt;-4&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|8&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|2.80x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|16&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|4.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|32&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|1.00x10&amp;lt;sup&amp;gt;-6&amp;lt;/sup&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
|64&lt;br /&gt;
|&amp;lt;nowiki&amp;gt;-40.9264&amp;lt;/nowiki&amp;gt;&lt;br /&gt;
|0&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
[[File:Helmholtz_Gridsize.png|thumb|400px|Image 2. Convergence of Helmholtz Free Energy Values with increasing grid sizes.|none]]&lt;br /&gt;
&lt;br /&gt;
==== Thermal Expansion of MgO ====&lt;br /&gt;
&lt;br /&gt;
[[File:HelmholtzTemp egn14.png|thumb|Image 3. Plot of Helmholtz free energy as a function of temperature.|480x480px|none]][[File:LatParamTemp egn14.png|thumb|Image 4. Plot of lattice parameter as a function of temperature.|480x480px|right]]&lt;br /&gt;
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From the plots in images 4 and 5, it can be seen that there is an increase in lattice parameter and hence increase in cell volume with increasing temperature. i.e Thermal expansion of the MgO lattice occurs.&lt;br /&gt;
It follows from this that the Helmholtz free energy becomes more negative with increasing temperature as can be seen in the plot of Image 3. This is due to the positive change in entropy (deltaS) associated with thermal expansion as the system becomes less configurationally constrained and hence more disordered. The -TdeltaS contribution to the Helmholtz free energy is thus negative and becomes progressively more negative with increasing temperature. &lt;br /&gt;
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The coefficient of thermal expansion is defined as: &lt;br /&gt;
&amp;lt;math&amp;gt;&lt;br /&gt;
\alpha_V = \frac{1}{V_0}\,\left(\frac{\partial V}{\partial T}\right)_p&lt;br /&gt;
&amp;lt;/math&amp;gt;&lt;br /&gt;
, where V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; represents the initial lattice volume.&lt;br /&gt;
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Using V&amp;lt;sub&amp;gt;0&amp;lt;/sub&amp;gt; = 18.8364 Å and the gradient from the plot of cell volume against temperature at constant pressure, the coefficient of thermal expansion α&amp;lt;sub&amp;gt;V&amp;lt;/sub&amp;gt; was found to be 2.654x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. The experimental values for a similar temperature range of 300 to 1000 K found in literature was 3.99x10&amp;lt;sup&amp;gt;-5&amp;lt;/sup&amp;gt; K&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;.&amp;lt;ref&amp;gt; O.L. Anderson and K. Zou, J Phys Chem Ref Data, 1990, &#039;&#039;&#039;19&#039;&#039;&#039;, 71&amp;lt;/ref&amp;gt; This has the same order of magnitude as the computed coefficient of thermal expansion and both values were in agreement.&lt;br /&gt;
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[[File:LatVolTemp egn14.png|thumb|Image 5. Plot of cell volume as a function of temperature.|505x505px|none]]&lt;br /&gt;
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=== Molecular Dynamics ===&lt;/div&gt;</summary>
		<author><name>Egn14</name></author>
	</entry>
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