VASP Computing Bulk Modulus of Si - Revision history

Yanmingw: /* Analyze data */

2015-09-04T08:10:07Z

Analyze data

@@ Line 134: / Line 134: @@
 When the simulation is finished, it will create data files <tt>Elatt.B.dat</tt> and <tt>platt.B.dat</tt>.
 <pre>
 .382 1  -.11953275E+02  -.11953296E+02 -.119533E+02
@@ Line 153: / Line 156: @@
 </pre>
  [a0, Ecoh, B] = fit_a0EB('Elatt.B.dat',2,8);
  fit_a0B ('platt.B.dat');
-The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus.  The second line fits the pressure data to a linear curve and computes the equilibrium lattice constant and bulk modulus.  In this example, the result is a0 = 5.389 angstrom, Ecoh = -5.977 eV, B = 95 GPa.
+The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus.  The second line fits the pressure data to a linear curve and computes the equilibrium lattice constant and bulk modulus.  In this example with US-LDA PP, the results are a0 = 5.389 angstrom, Ecoh = -5.977 eV, B = 95 GPa.

Yanmingw: /* Analyze data */

2015-09-04T08:06:01Z

Analyze data

@@ Line 133: / Line 133: @@
 When the simulation is finished, it will create data files <tt>Elatt.B.dat</tt> and <tt>platt.B.dat</tt>.
 Launch <tt>octave</tt> and run the following functions [[media:fit_a0EB.m.txt | fit_a0EB.m]] and [[media:fit_a0B.m.txt | fit_a0B.m]],
- fit_a0EB('Elatt.B.dat');
+ [a0, Ecoh, B] = fit_a0EB('Elatt.B.dat',2,8);
  fit_a0B ('platt.B.dat');

Yanmingw at 05:56, 2 September 2015

2015-09-02T05:56:10Z

← Older revision		Revision as of 05:56, 2 September 2015
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	</pre>		</pre>

	'''POSCAR ~~example for Si~~'''		'''POSCAR'''

			Here's one example for Si, which will be automatically rewritten every iteration.
	<pre>		<pre>
	POSCAR for DC Si (created manually)		POSCAR for DC Si (created manually)

Yanmingw: /* Run VASP */

2015-09-02T02:47:25Z

Run VASP

← Older revision		Revision as of 02:47, 2 September 2015
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	$a universal scaling factor		$a universal scaling factor
	0.0 0.5 0.5		0.0 0.5 0.5
	0.5 0.0 0.5		0.5 0.0 0.5
	0.5 0.5 0.0		0.5 0.5 0.0
	2		2
	Direct		Direct
	-0.125 -0.125 -0.125		-0.125 -0.125 -0.125

Yanmingw at 02:38, 2 September 2015

2015-09-02T02:38:03Z

← Older revision		Revision as of 02:38, 2 September 2015
Line 131:		Line 131:
	===Analyze data===		===Analyze data===

	~~After~~ ~~running~~ it as ~~<tt>./auto.B.serial</tt>~~, it will create data files <tt>Elatt.B.dat</tt> and <tt>platt.B.dat</tt>.		When the simulation is finished, it will create data files <tt>Elatt.B.dat</tt> and <tt>platt.B.dat</tt>.

	Launch <tt>octave</tt> and run the following functions [[media:fit_a0EB.m.txt \| fit_a0EB.m]] and [[media:fit_a0B.m.txt \| fit_a0B.m]],		Launch <tt>octave</tt> and run the following functions [[media:fit_a0EB.m.txt \| fit_a0EB.m]] and [[media:fit_a0B.m.txt \| fit_a0B.m]],
Line 139:		Line 139:

	The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus. The second line fits the pressure data to a linear curve and computes the equilibrium lattice constant and bulk modulus. In this example, the result is a0 = 5.389 angstrom, Ecoh = -5.977 eV, B = 95 GPa.		The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus. The second line fits the pressure data to a linear curve and computes the equilibrium lattice constant and bulk modulus. In this example, the result is a0 = 5.389 angstrom, Ecoh = -5.977 eV, B = 95 GPa.

	===Parallel computation===

	To run <tt>vasp</tt> in parallel, you need to submit [[media:vasp.pbs.txt \| vasp.pbs]] as

	qsub vasp.pbs


	You will need the following two files to do this calculation in parallel on SU-AHPCRC:
	[[media:auto.B.par.Au.txt \| auto.B.par]] and
	[[media:B.pbs.Au.txt \| B.pbs]].

Yanmingw: /* Run VASP */

2015-09-02T02:36:50Z

Run VASP

← Older revision		Revision as of 02:36, 2 September 2015
Line 125:		Line 125:
	</pre>		</pre>

	To submit the job, prepare the '''vasp.pbs''' file with the above content and put it in the same folder that contains the '''INCAR'''', '''POTCAR''', '''KPOINTS''' files. From this folder, type		To submit the job, prepare the '''vasp.pbs''' file with the above content and put it in the same folder that contains the '''INCAR''', '''POTCAR''', '''KPOINTS''' files. From this folder, type

	qsub vasp.pbs		qsub vasp.pbs

Yanmingw: /* Run VASP */

2015-09-02T02:36:16Z

Run VASP

← Older revision		Revision as of 02:36, 2 September 2015
Line 63:		Line 63:
	===Run VASP===		===Run VASP===

			We can write one .pbs script to submit the VASP simulation request to the cluster.
	Now we are ready to run

		⚫	Using MC2 cluster as an example, we provide the following <tt>vasp.pbs</tt> for the calculation of equilibrium lattice constant, cohesive energy and bulk modulus. The goal of this script is to run <tt>vasp</tt> in iterations with different lattice constants.
	vasp

⚫	To ~~compute~~ the equilibrium lattice constant, cohesive energy and bulk modulus, we ~~use~~ ~~the~~ ~~following~~ script ~~<tt>auto.B.serial</tt>~~ to run <tt>vasp</tt> ~~repeated~~ with different lattice constants.

	<pre>		<pre>
Line 126:		Line 124:
	done		done
	</pre>		</pre>

			To submit the job, prepare the '''vasp.pbs''' file with the above content and put it in the same folder that contains the '''INCAR'''', '''POTCAR''', '''KPOINTS''' files. From this folder, type

			qsub vasp.pbs

	===Analyze data===		===Analyze data===

Yanmingw: /* Input files */

2015-09-02T01:48:17Z

Input files

← Older revision		Revision as of 01:48, 2 September 2015
Line 52:		Line 52:
	Direct		Direct
	-0.125 -0.125 -0.125		-0.125 -0.125 -0.125
	0.125 0.125 0.125		0.125 0.125 0.125
	</pre>		</pre>

Yanmingw: /* Input files */

2015-09-02T01:47:46Z

Input files

← Older revision		Revision as of 01:47, 2 September 2015
Line 47:		Line 47:
	5.431 universal scaling factor		5.431 universal scaling factor
	0.0 0.5 0.5		0.0 0.5 0.5
	0.5 0.0 0.5		0.5 0.0 0.5
	0.5 0.5 0.0		0.5 0.5 0.0
	2		2
	Direct		Direct
	-0.125 -0.125 -0.125		-0.125 -0.125 -0.125
	0.125 0.125 0.125		0.125 0.125 0.125
	</pre>		</pre>

Yanmingw: /* Input files */

2015-09-02T01:47:17Z

Input files

← Older revision		Revision as of 01:47, 2 September 2015
Line 45:		Line 45:
	<pre>		<pre>
	POSCAR for DC Si (created manually)		POSCAR for DC Si (created manually)
			5.431 universal scaling factor
	???
	0 0.5 0.5		0.0 0.5 0.5
	0.5 0 0.5		0.5 0.0 0.5
	0.5 0.5 0		0.5 0.5 0.0
	1		2
			Direct
	Cartesian (real coordinates r)
			-0.125 -0.125 -0.125
	0 0 0		0.125 0.125 0.125
	</pre>		</pre>

Line 59:		Line 60:

	https://www.vasp.at/vasp-workshop/slides/pseudoppdatabase.pdf		https://www.vasp.at/vasp-workshop/slides/pseudoppdatabase.pdf

	===Run VASP===		===Run VASP===