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		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599976</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599976"/>
		<updated>2017-03-10T09:54:14Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why two of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The lattice parameter, and volume, increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph shown above, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using Molecular Dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599947</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599947"/>
		<updated>2017-03-10T09:45:09Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Computing the Phonons of the MgO Lattice */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why two of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The lattice parameter, and volume, increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using Molecular Dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599927</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599927"/>
		<updated>2017-03-10T09:41:08Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Molecular Dynamics Calculations */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why two of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The lattice parameter, and volume, increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using Molecular Dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599750</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599750"/>
		<updated>2017-03-10T03:44:54Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why two of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The lattice parameter, and volume, increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599743</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599743"/>
		<updated>2017-03-10T03:38:54Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why two of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599742</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599742"/>
		<updated>2017-03-10T03:38:18Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points  and 2 non-degenerate points. This degeneracy explains why ttwo of the peaks are twice the size of the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599741</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599741"/>
		<updated>2017-03-10T03:35:13Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Introduction */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons are discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599740</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599740"/>
		<updated>2017-03-10T03:34:21Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Computing the Phonons of the MgO Lattice */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient. In the case of lithium, it is a very different system. With metallic bonding the lattice is made from the lithium cations, which are surrounded by electrons, often described as a ‘sea of electrons’. The repulsion of the lithium cations is lowered due to the electrons, which lowers the energy of dispersion and allows for a smaller grid size to be used.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599735</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599735"/>
		<updated>2017-03-10T03:09:29Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* The Thermal Expansion of MgO */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. This difference is likely due to the limitations of the quasi-harmonic approximation previously mentioned and the fact that a truly accurate result would require an infinite grid size.&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599734</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599734"/>
		<updated>2017-03-10T03:07:54Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Conclusions */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
From the calculations run in this computational experiment, several observations can be made. It was shown that with the increase in temperature of an MgO crystal the lattice constant, and therefore also the cell volume, will increase. It can be seen that in a high temperature system the MD method should be used as it is a more realistic model, especially if the temperature is approaching the point at with the bonds will dissociate. For low temperatures, however, the quasi-harmonic model is sufficient to provide a reasonably accurate answer.&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599733</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599733"/>
		<updated>2017-03-10T02:55:44Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors are increased the DOS smooths out due to more &#039;&#039;&#039;k&#039;&#039;&#039;-points being accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599726</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599726"/>
		<updated>2017-03-10T02:22:45Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Methodology */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
RedHat Linux was the operating system used to run all the calculations. Within Linux, the DLVisualize program was used to interface with the models of the MgO system and the General Utility Lattice Program (GULP) was used to simulate the properties of the system. The phonon dispersion curve was calculated using 50 points in the k-space and the density of states graphs were calculated at a constant pressure. The free energies were calculated at a constant temperature of 300 K. For the molecular dynamics simulations, the ensemble was set to NPT, the time-step to 1 femtosecond, equilibrium and production steps to 500 and the sampling steps, as well as the trajectory steps to 5 each.&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599725</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599725"/>
		<updated>2017-03-10T02:20:39Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Molecular Dynamics Calculations */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The thermal expansion coefficient found from the MD calculations is 3.213x10-5 K-1. This number is closer to the one found in literature. This is likely due to the MD calculations being closer to what happens in the real world. Another advantage of MD simulations over the quasi-harmonic is that when the temperature reaches the melting point of the crystal the bonds would break.&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599721</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599721"/>
		<updated>2017-03-10T01:51:41Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Phonons and discrete ‘packets’ of vibrational energy.  Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599713</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599713"/>
		<updated>2017-03-10T01:32:47Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1,&amp;lt;ref name=&amp;quot;alpha&amp;quot; /&amp;gt; which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;alpha&amp;quot;&amp;gt;S.S. Kushwah, J. Shanker, &#039;&#039;Physica B&#039;&#039;, 1996, &#039;&#039;&#039;225&#039;&#039;&#039;, pp. 283-287.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599712</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599712"/>
		<updated>2017-03-10T01:30:51Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Molecular Dynamics Calculations */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1, which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
Using molecular dynamics (MD) to compute the calculations allows the system to behave as they would in the real world, in accordance to Newton’s Laws. However, for an MD calculation a supercell needs to be used as if a single cell is used the movements in the system would all be perfectly in phase and is not a good representation of real world physics. &lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599710</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599710"/>
		<updated>2017-03-10T01:27:37Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Molecular Dynamics Calculations */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1, which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599709</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599709"/>
		<updated>2017-03-10T01:26:29Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1, which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
[[File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png|thumb|centre|500px|Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Quasi-Harmonic_and_Molecular_Dynamics_Primitive_Cell_Volumes_against_Temperature_cet114.png&amp;diff=599707</id>
		<title>File:Quasi-Harmonic and Molecular Dynamics Primitive Cell Volumes against Temperature cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Quasi-Harmonic_and_Molecular_Dynamics_Primitive_Cell_Volumes_against_Temperature_cet114.png&amp;diff=599707"/>
		<updated>2017-03-10T01:25:13Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599698</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599698"/>
		<updated>2017-03-10T01:11:27Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
The calculated coefficient is 2.671x10-5 K-1. The &amp;lt;math&amp;gt;\alpha&amp;lt;/math&amp;gt; coefficient found in literature is 4.47x10-5 K-1, which was taken at 1000 K. While the two are of the same order, there is a clear difference between them. &lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599697</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599697"/>
		<updated>2017-03-10T01:04:14Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system. At high temperatures the approximation breaks down, as it assumes that the bonds will never break and simply vibrate more and more, meaning even at the melting point of the crystal the bonds would still be unbroken. With an exactly harmonic diatomic molecule, the bond lengths do not change as the equilibrium position stays the same as the energy increases.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599691</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599691"/>
		<updated>2017-03-10T00:52:51Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The Helmholtz equation shows that as the temperature increases, the magnitude of the negative term increases, which explains the increased negativity of the free energy. In the cases of the lattice parameter and volume, they increase as the temperature does. This is because these computations are run using the quasi-harmonic approximation, where an increase in temperature moves the system up an anharmonic, Morse-like potential and results in the bond lengths increasing. The plots are not completely linear due to the zero-point energy assumed in the system.&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599665</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599665"/>
		<updated>2017-03-10T00:38:13Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. Using the quasi-harmonic approximation, the MgO free energy was computed with respect to the temperature of the system. The free energy, lattice constants and primitive cell volume were plotted against temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599652</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599652"/>
		<updated>2017-03-10T00:27:39Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
The equation for the Helmholtz free energy is &amp;lt;math&amp;gt;A=U-TS&amp;lt;/math&amp;gt;. This equation can be simplified to &amp;lt;math&amp;gt;dA=-PdV-SdT&amp;lt;/math&amp;gt;, showing that the free energy is dependent on both temperature and volume. The free energy was plotted against temperature and the lattice constant, which is related to the volume, was also plotted against the temperature.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599619</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599619"/>
		<updated>2017-03-10T00:05:34Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599613</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599613"/>
		<updated>2017-03-10T00:02:22Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
The aims of this computational experiment are to compute the phonon dispersion curve, density of states, free energy and thermal expansion of magnesium oxide, MgO. Both the quasi-harmonic approximation and a molecular dynamics simulation are used, and the results from both compared.&lt;br /&gt;
&lt;br /&gt;
The system being analysed is the MgO crystal. The conventional cell is made up of 8 atoms, has a face centred cubic (fcc) structure and parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is made up of 2 atoms, has the parameters a&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;p&amp;lt;/sub&amp;gt; and is the smallest possible way of representing the crystal lattice. Below is a diagram showing how the two cells are related.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599520</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599520"/>
		<updated>2017-03-09T23:31:56Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599296</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599296"/>
		<updated>2017-03-09T21:55:18Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
By looking at the linear region, between 300 and 1000 K, of the graph where cell volume is plotted against temperature, the thermal expansion coefficient, &amp;lt;math&amp;gt; \alpha&amp;lt;/math&amp;gt;, can be calculated using the equation &amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;.&lt;br /&gt;
he calculated coefficient is 2.671x10-5 K-1&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599234</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599234"/>
		<updated>2017-03-09T21:31:20Z</updated>

		<summary type="html">&lt;p&gt;Cet114: /* Using the Harmonic Approximation to Calculate the Free Energy */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
Using the quasi-harmonic approximation, the free energy is calculated in relation to an increasing k-point grid by summing all the normal modes of vibration. By comparing the results of increased grid sizes, the best compromise between experimental time and answer accuracy can be found.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:right&amp;quot;&amp;gt;&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599208</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599208"/>
		<updated>2017-03-09T21:20:12Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599031</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599031"/>
		<updated>2017-03-09T19:26:59Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;math&amp;gt; \alpha={1 \over V_0} \Bigg( {\partial V\over \partial T}\Bigg)_P &amp;lt;/math&amp;gt;&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599007</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=599007"/>
		<updated>2017-03-09T19:13:09Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
! Free Energy against Temperature !! Lattice Constants against Temperature&lt;br /&gt;
|- &lt;br /&gt;
| [[File:Free Energy against Temperature cet114.png|centre|500px]] || [[File:Lattice Constants against Temperature cet114.png|centre|500px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
[[File:Primitive Cell Volume against Temperature cet114.png|thumb|centre|500px|Primitive Cell Volume against Temperature]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitive_Cell_Volume_against_Temperature_cet114.png&amp;diff=599003</id>
		<title>File:Primitive Cell Volume against Temperature cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Primitive_Cell_Volume_against_Temperature_cet114.png&amp;diff=599003"/>
		<updated>2017-03-09T19:11:00Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Lattice_Constants_against_Temperature_cet114.png&amp;diff=598980</id>
		<title>File:Lattice Constants against Temperature cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Lattice_Constants_against_Temperature_cet114.png&amp;diff=598980"/>
		<updated>2017-03-09T18:56:02Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Free_Energy_against_Temperature_cet114.png&amp;diff=598977</id>
		<title>File:Free Energy against Temperature cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Free_Energy_against_Temperature_cet114.png&amp;diff=598977"/>
		<updated>2017-03-09T18:54:51Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598964</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598964"/>
		<updated>2017-03-09T18:47:42Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å.&amp;lt;ref name=&amp;quot;CaO&amp;quot; /&amp;gt; The lattice constant of MgO is 4.209 Å&amp;lt;ref name=&amp;quot;MgO&amp;quot; /&amp;gt;, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å.&amp;lt;ref name=&amp;quot;Faujasite&amp;quot; /&amp;gt; It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;CaO&amp;quot;&amp;gt;K. Doll, M. Dolg and H. Stoll, &#039;&#039;Physical Review B&#039;&#039;, 1996, &#039;&#039;&#039;54&#039;&#039;&#039;, pp. 13529-13535.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;MgO&amp;quot;&amp;gt;A. Cimino, P. Porta and M. Valigi, &#039;&#039;Journal of The American Ceramic Society&#039;&#039;, &#039;&#039;&#039;49&#039;&#039;&#039;, pp. 152-156.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;Faujasite&amp;quot;&amp;gt;D. N. Stamires, &#039;&#039;Clays and Clay Minerals&#039;&#039;, 1973, &#039;&#039;&#039;21&#039;&#039;&#039;, pp. 379-389.&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598947</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598947"/>
		<updated>2017-03-09T18:41:51Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å. The lattice constant of MgO is 4.209 Å, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å. It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;br /&gt;
&amp;lt;ref name=&amp;quot;1.0&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&amp;lt;references&amp;gt;&lt;br /&gt;
&amp;lt;ref name=&amp;quot;1.0&amp;quot;&amp;gt;Thing&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;/references&amp;gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598940</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598940"/>
		<updated>2017-03-09T18:37:45Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ DOS of Different Grid Sizes&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å. The lattice constant of MgO is 4.209 Å, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å. It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
[[File:Free Energy against K-point Grid Size cet114.png|thumb|right|450px|Free Energy against K-point Grid Size]]&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Free Energies of Different Grid Sizes&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is seen from the table and graph above that initially there is a relatively dramatic change to the free energy with an increase in grid size. After a grid size of 8x8x8 the free energy is reasonably stable, however when you reach a size of 64x64x64 it remains the same as the 32x32x32 at 8 significant figures. For this reason, a grid size of 32x32x32 provides an accurate enough result and takes less time to run than the calculation with a 64x64x64 grid.&lt;br /&gt;
For free energy calculations that are accurate to 1meV and 0.5 meV, a grid size of 3x3x3 can be used, and for an energy accurate to 0.1meV a grid size of 8x8x8 could be used.&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:Free_Energy_against_K-point_Grid_Size_cet114.png&amp;diff=598932</id>
		<title>File:Free Energy against K-point Grid Size cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:Free_Energy_against_K-point_Grid_Size_cet114.png&amp;diff=598932"/>
		<updated>2017-03-09T18:30:43Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598904</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598904"/>
		<updated>2017-03-09T18:13:16Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Various Cell Representations of MgO&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
Calcium Oxide (CaO) has a very similar lattice to MgO. It is made up of Ca&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 held in an ionic lattice, with a lattice constant of 4.803 Å. The lattice constant of MgO is 4.209 Å, meaning that the CaO is slightly larger. As it is larger in real space, it is smaller in reciprocal space and therefore requires less &#039;&#039;&#039;k&#039;&#039;&#039;-points meaning a marginally smaller grid size could be used, however 32x32x32 would still work well. The Zeolite Faujasite is far larger than MgO, with lattice constant of 24.66 Å. It is so much lager in real space that a much smaller &#039;&#039;&#039;k&#039;&#039;&#039;-point grid would be sufficient.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Various Cell Representations of MgO&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598851</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598851"/>
		<updated>2017-03-09T17:52:52Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In order to plot an accurate DOS, all the &#039;&#039;&#039;k&#039;&#039;&#039;-points need to be included. This can be achieved by increasing the shrinking factors and enlarging the grid of &#039;&#039;&#039;k&#039;&#039;&#039;-points. The most accurate result would be obtained by using a grid of infinite size, however as this not possible the grid sizes 2x2x2, 3x3x3, 4x4x4, 8x8x8, 16x6x16, 32x32x32 and 64x64x64 were calculated.&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Various Cell Representations of MgO&lt;br /&gt;
! 2x2x2 !! 3x3x3 !! 4x4x4 !! 8x8x8&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 2x2x2 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 3x3x3 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 4x4x4 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 8x8x8 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+&lt;br /&gt;
!16x16x16 !! 32x32x32 !! 64x64x64&lt;br /&gt;
|-&lt;br /&gt;
| [[File:MgO Phonon DOS 16x16x16 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 32x32x32 cet114.png|centre|250px]] || [[File:MgO Phonon DOS 64x64x64 cet114.png|centre|250px]]&lt;br /&gt;
|}&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
As the shrinking factors increase the DOS smooths out as more &#039;&#039;&#039;k&#039;&#039;&#039;-points are accessed. From comparing the graphs, it can be seen that the DOS with a 32x32x32 grid size gives a result similar to the 64x64x64 grid size DOS, and so is the minimum grid size that should be used in these calculations.&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Various Cell Representations of MgO&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_64x64x64_cet114.png&amp;diff=598842</id>
		<title>File:MgO Phonon DOS 64x64x64 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_64x64x64_cet114.png&amp;diff=598842"/>
		<updated>2017-03-09T17:49:31Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_32x32x32_cet114.png&amp;diff=598841</id>
		<title>File:MgO Phonon DOS 32x32x32 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_32x32x32_cet114.png&amp;diff=598841"/>
		<updated>2017-03-09T17:49:16Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_16x16x16_cet114.png&amp;diff=598839</id>
		<title>File:MgO Phonon DOS 16x16x16 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_16x16x16_cet114.png&amp;diff=598839"/>
		<updated>2017-03-09T17:48:59Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_8x8x8_cet114.png&amp;diff=598838</id>
		<title>File:MgO Phonon DOS 8x8x8 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_8x8x8_cet114.png&amp;diff=598838"/>
		<updated>2017-03-09T17:48:46Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_4x4x4_cet114.png&amp;diff=598836</id>
		<title>File:MgO Phonon DOS 4x4x4 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_4x4x4_cet114.png&amp;diff=598836"/>
		<updated>2017-03-09T17:48:31Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
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&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_3x3x3_cet114.png&amp;diff=598835</id>
		<title>File:MgO Phonon DOS 3x3x3 cet114.png</title>
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		<updated>2017-03-09T17:48:17Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
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		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_2x2x2_cet114.png&amp;diff=598830</id>
		<title>File:MgO Phonon DOS 2x2x2 cet114.png</title>
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		<updated>2017-03-09T17:46:49Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
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		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598786</id>
		<title>Rep:CeT114MgO</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:CeT114MgO&amp;diff=598786"/>
		<updated>2017-03-09T17:32:48Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
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&lt;div&gt;=The Free Energy and Thermal Expansion of MgO=&lt;br /&gt;
&lt;br /&gt;
==Introduction==&lt;br /&gt;
&lt;br /&gt;
Mg&amp;lt;sub&amp;gt;2+&amp;lt;/sub&amp;gt; and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The vibrational phonons of a crystal can be used to find its thermal expansion, phonon dispersion and vibrational density of states, DOS. In this computational experiment, Magnesium Oxide, MgO, is studied. MgO crystals are an ionic lattice made up of Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anions. The MgO lattice can be described either by its conventional cell, which contains 8 atoms, or its primitive cell, which contains 2. The conventional cell is face-centred-cubic, fcc, with the lattice parameters a&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=b&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;=c&amp;lt;sub&amp;gt;c&amp;lt;/sub&amp;gt;. The primitive cell is the smallest possible representation of the crystal, and can be seen by drawing a rhombic structure inside the conventional cell with the 8 vertices being Mg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; cations and an O&amp;lt;sup&amp;gt;2-&amp;lt;/sup&amp;gt; anion at its centre. For crystal structures it is assumed they are perfect, without defects and periodic across an infinite three dimensional system. The cells are shown below.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Types of MgO Lattice Cells&lt;br /&gt;
! Conventional Cell !! Primitive Cell !! Primitive Cell shown inside the Conventional&lt;br /&gt;
|-&lt;br /&gt;
| [[File:Conventional cell cet114.png|300px]] || [[File:Primitive cell cet114.png|300px]] || [[File:Primitive cell inside the conventional cet114.png|300px]]&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Methodology===&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
==Results and Discussions==&lt;br /&gt;
&lt;br /&gt;
===Computing the Phonons of the MgO Lattice===&lt;br /&gt;
The phonon dispersion curve of the MgO lattice was computed to inspect its normal modes of vibration, or phonon modes. A phonon dispersion curve shows the possible frequencies of the phonon modes at a particular wave-vector, &#039;&#039;&#039;k&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon dispersion cet114.png|thumb|centre|500px|Phonon Dispersion Curve of MgO]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
A Density of States (DOS) graph can be plotted when all the k-points are summed. A DOS was calculated for a grid with shrinking factors 1x1x1, which has a single &#039;&#039;&#039;k&#039;&#039;&#039;-point. The DOS graph has 4 peaks and relates to the &#039;&#039;&#039;L&#039;&#039;&#039; &#039;&#039;&#039;k&#039;&#039;&#039;-point in the dispersion curve, with 2 degenerate points at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;, and 2 non-degenerate points at 676 and 819 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt;. This degeneracy explains why the peaks at 288 and 352 cm&amp;lt;sup&amp;gt;-1&amp;lt;/sup&amp;gt; are twice the size as the other two peaks.&lt;br /&gt;
&lt;br /&gt;
[[File:MgO Phonon DOS 1x1x1 cet114.png|thumb|centre|500px|DOS of MgO with shrinking factors 1x1x1]]&lt;br /&gt;
&amp;lt;br style=&amp;quot;clear:left&amp;quot;&amp;gt;&lt;br /&gt;
&lt;br /&gt;
===Using the Harmonic Approximation to Calculate the Free Energy===&lt;br /&gt;
&lt;br /&gt;
{| class=&amp;quot;wikitable&amp;quot; border=&amp;quot;1&amp;quot;&lt;br /&gt;
|+ Various Cell Representations of MgO&lt;br /&gt;
! k-space grid !! Free Energy&lt;br /&gt;
|-&lt;br /&gt;
| 1x1x1 || -40.930301&lt;br /&gt;
|-&lt;br /&gt;
| 2x2x2 || -40.926609&lt;br /&gt;
|-&lt;br /&gt;
| 3x3x3 || -40.926432  &lt;br /&gt;
|-&lt;br /&gt;
| 4x4x4 || -40.926450&lt;br /&gt;
|-&lt;br /&gt;
| 8x8x8 || -40.926478  &lt;br /&gt;
|-&lt;br /&gt;
| 16x16x16 || -40.926482 &lt;br /&gt;
|-&lt;br /&gt;
| 32x32x32 || -40.926483&lt;br /&gt;
|-&lt;br /&gt;
| 64x64x64 || -40.926483&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
===The Thermal Expansion of MgO===&lt;br /&gt;
&lt;br /&gt;
===Molecular Dynamics Calculations===&lt;br /&gt;
&lt;br /&gt;
==Conclusions==&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
	<entry>
		<id>https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_1x1x1_cet114.png&amp;diff=598753</id>
		<title>File:MgO Phonon DOS 1x1x1 cet114.png</title>
		<link rel="alternate" type="text/html" href="https://chemwiki.ch.ic.ac.uk/index.php?title=File:MgO_Phonon_DOS_1x1x1_cet114.png&amp;diff=598753"/>
		<updated>2017-03-09T17:19:46Z</updated>

		<summary type="html">&lt;p&gt;Cet114: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Cet114</name></author>
	</entry>
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