VASP Computing Elastic Constants of Au - Revision history

Yanmingw: /* Analyze data */

2015-09-06T05:42:41Z

Analyze data

← Older revision		Revision as of 05:42, 6 September 2015
Line 255:		Line 255:
	The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively. The first '''4''' specifies the number of atoms in the computation cell and the second '''4''' is the number of atoms in a conventional unit cell.		The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively. The first '''4''' specifies the number of atoms in the computation cell and the second '''4''' is the number of atoms in a conventional unit cell.
	The second lines computes the C11 and C12 elastic constants and the third line calculates C44. Suggested results are C11 = 206 GPa, C12 = 176 GPa and C44 = 36 GPa for calculations with US-LDA PP.		The second lines computes the C11 and C12 elastic constants and the third line calculates C44. Suggested results are C11 = 206 GPa, C12 = 176 GPa and C44 = 36 GPa for calculations with US-LDA PP.

			<span style="background:yellow"> '''C44 of 36 GPa is a bit lower than the paper's result of 47 GPa (The experimental value is 45 GPa).''' </span>

Yanmingw at 09:31, 4 September 2015

2015-09-04T09:31:52Z

@@ Line 3: / Line 3: @@
 VASP: Computing Elastic Constants of Au</STRONG></font></P>
 <DIV>
-<P ALIGN="CENTER"><STRONG> </STRONG></P>
+<P ALIGN="CENTER"><STRONG> Modified by Yanming Wang (Sep, 2015)</STRONG></P>
 </DIV>
@@ Line 215: / Line 215: @@
 ===Analyze data===
-After running the two scripts above for C11 and C44, <tt>./auto.B.serial</tt> it will create the data files: <tt>Elatt.C11.dat</tt>,<tt>platt.C11.dat</tt>, <tt>Elatt.C44.dat</tt>,  and <tt>platt.C44.dat</tt>.
+After running the two scripts above for C11 and C44, the data files: <tt>Elatt.C11.dat</tt> and  <tt>Elatt.C44.dat</tt> will be created.

Yanmingw: /* Run VASP */

2015-09-04T09:25:33Z

Run VASP

← Older revision		Revision as of 09:25, 4 September 2015
Line 87:		Line 87:
	===Run VASP===		===Run VASP===

	To compute the elastic constants we ~~use~~ the following ~~script~~ <tt>~~auto~~.B.~~serial~~</tt> to run <tt>vasp</tt> repeated with different values for the first ~~C11~~ component of the first Bravais lattice vector, '''$a'''. ~~Make~~ ~~sure~~ ~~you~~ ~~have~~ ~~previously calculated~~ the ~~equilibrium~~ lattice constant ~~for~~ ~~this~~ ~~supercell~~ ~~with~~ 4 ~~atoms~~, ~~otherwise~~ ~~errors~~ in ~~the~~ ~~calculations~~ ~~could~~ ~~arise.~~ ~~The~~ ~~script~~ ~~creates~~ ~~automatically~~ the ~~POSCAR~~ ~~file~~ as in the ~~example~~ ~~above~~ for every '''a''' ~~especified~~ in the script in the range from 0.997 to 1.003. For C44 ~~script~~ the $a value is ~~changed~~ for the first and ~~the~~ second ~~components~~ of the first Bravais lattice vector.		To compute the elastic constants, we prepared the following PBS scripts to submit the jobs to MC2 cluster. <tt>vasp.pbs.C11</tt> is used to to run <tt>vasp</tt> repeated with different values for the first component of the first Bravais lattice vector, '''$a'''. Here we put 4.067877 as the length of the lattice constant in the script, which is obtained from our previous VASP calculation. In generally, you are expected to put a reliable value from your lattice constant calculation with the same PP. The script automatically creates the POSCAR file for every '''a''' specified in the script in the range from 0.997 to 1.003. For C44 calculation, the PBS script <tt>vasp.pbs.C44</tt> changes the value of '''$a''' for the first and second component of the first Bravais lattice vector.

	'''Script for C11'''		'''PBS Script for C11'''

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
			#PBS -N vasp.Au.C11
			#PBS -j oe
			#PBS -l nodes=1:ppn=8,walltime=48:00:00
			#PBS -V

			### ---------------------------------------
			### BEGINNING OF EXECUTION
			### ---------------------------------------

			echo The master node of this job is `hostname`
			echo The working directory is `echo $PBS_O_WORKDIR`
			echo This job runs on the following nodes:
			echo `cat $PBS_NODEFILE`

			ncpu=`cat $PBS_NODEFILE \| wc -w`
			echo "Number of processors = $ncpu "

			### end of information preamble

			cd $PBS_O_WORKDIR

		⚫	echo $PWD

			cd $PBS_O_WORKDIR

			module load vasp

	rm WAVECAR		rm WAVECAR
	for a in 0.997 0.998 0.999 1.000 1.001 1.002 1.003		for a in 0.997 0.998 0.999 1.000 1.001 1.002 1.003
Line 98:		Line 125:
	cat > POSCAR << FIN		cat > POSCAR << FIN
	POSCAR for FCC Au		POSCAR for FCC Au
	4.~~062241~~ accurate equilibrium lattice constant		4.067877 accurate equilibrium lattice constant
	$a 0.0 0.0 first Bravais lattice vector		$a 0.0 0.0 first Bravais lattice vector
	0.0 1.0 0.0 second Bravais lattice vector		0.0 1.0 0.0 second Bravais lattice vector
Line 111:		Line 138:
	FIN		FIN

	echo "a=$a"		echo "a=$a ncpu=$ncpu"

	./vasp
			cmd="mpiexec -np $ncpu vasp"
			$cmd >& vasp.log

	E=`tail -1 OSZICAR`		E=`tail -1 OSZICAR`
	echo $a $E \| sed -s 's/F=//; s/E0=//; s/d E =//;' >> Elatt.C11.dat		echo $a $E \| sed -s 's/F=//; s/E0=//; s/d E =//;' >> Elatt.C11.dat

	p=`grep pressure OUTCAR \| cut -b 25-34`
	echo $a $p >> platt.C11.dat

	done		done
	</pre>		</pre>

	'''~~Script~~ for C44'''		'''PBS script for C44'''

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
			#PBS -N vasp.Au.C44
			#PBS -j oe
			#PBS -l nodes=1:ppn=8,walltime=48:00:00
			#PBS -V

			### ---------------------------------------
			### BEGINNING OF EXECUTION
			### ---------------------------------------

			echo The master node of this job is `hostname`
			echo The working directory is `echo $PBS_O_WORKDIR`
			echo This job runs on the following nodes:
			echo `cat $PBS_NODEFILE`

			ncpu=`cat $PBS_NODEFILE \| wc -w`
			echo "Number of processors = $ncpu "

			### end of information preamble

			cd $PBS_O_WORKDIR

			echo $PWD

			cd $PBS_O_WORKDIR

			module load vasp

	rm WAVECAR		rm WAVECAR
	for a in 0.997 0.998 0.999 1.000 1.001 1.002 1.003		for a in 0.997 0.998 0.999 1.000 1.001 1.002 1.003
Line 132:		Line 185:
	cat > POSCAR << FIN		cat > POSCAR << FIN
	POSCAR for FCC Au		POSCAR for FCC Au
	4.~~062241~~ accurate equilibrium lattice constant		4.067877 accurate equilibrium lattice constant
	$a $a 0.0 first lattice vector		$a $a 0.0 first lattice vector
	-1.0 1.0 0.0 second lattice vector		-1.0 1.0 0.0 second lattice vector
Line 148:		Line 201:
	0.7500 0.2500 0.5000 T T T		0.7500 0.2500 0.5000 T T T
	FIN		FIN

⚫	echo ~~"a=~~$a"
			echo "a=$a ncpu=$ncpu"
	./vasp

			cmd="mpiexec -np $ncpu vasp"
			$cmd >& vasp.log

	E=`tail -1 OSZICAR`		E=`tail -1 OSZICAR`
	echo $a $E \| sed -s 's/F=//; s/E0=//; s/d E =//;' >> Elatt.C44.dat		echo $a $E \| sed -s 's/F=//; s/E0=//; s/d E =//;' >> Elatt.C44.dat

	p=`grep pressure OUTCAR \| cut -b 25-34`
	echo $a $p >> platt.C44.dat

	done		done

Yanmingw: /* Input files */

2015-09-04T09:20:46Z

Input files

← Older revision		Revision as of 09:20, 4 September 2015
Line 9:		Line 9:
	===Input files===		===Input files===

		⚫	Here we give an example of how to use VASP to compute the elastic constants C11, C12 and C44 of Au. We performed this calculation on <tt>MC2</tt> in PARALLEL mode in <tt>~/Codes/VASP/runs/Au_bulk_C11</tt> and <tt>~/Codes/VASP/runs/Au_bulk_C44</tt> two directories. Each directory contains the following files.
	'''(Under construction!!!)'''

⚫	Here we give an example of how to use VASP to compute the elastic constants C11 and C44 of ~~LDA-~~Au. We performed this calculation on <tt>~~MC-CC~~</tt> in PARALLEL ~~model~~ in ~~the~~ <tt>~/Codes/VASP/runs/Au/~~LDA~~/~~perfect.21x21x21~~</tt> ~~directory~~. ~~This~~ directory contains the following files.

	'''INCAR'''		'''INCAR'''

	<pre>		<pre>
			PREC = High
⚫	ENCUT = ~~400~~ or ~~500??~~

	ISIF = 2 It relaxes atoms but keep cell volume fixed!
	~~ISMEAR~~ = 1		ISTART = 0
			ICHARG = 2
			ISMEAR = 1
	SIGMA = 0.1		SIGMA = 0.1

			EDIFF = 1E-09
			NELM = 40
			ENMAX = 500
		⚫	ENCUT = 500

			ISIF = 2
			NSW = 100
			IBRION = 2
	</pre>		</pre>

Line 32:		Line 41:
	</pre>		</pre>

	'''POSCAR ~~example for C11~~'''		'''POSCAR '''

			Here's an example for Au C11 and C12 calculation, which will be changed later in PBS script every iteration.

	<pre>		<pre>
	POSCAR for FCC Au (created manually)		POSCAR for FCC Au (created manually)
	POSCAR for FCC Au		POSCAR for FCC Au
	4.~~062241~~ from acurate VASP lattice calculation		4.067877 from acurate VASP lattice calculation
	1.000 0.0 0.0 first Bravais lattice vector		1.000 0.0 0.0 first Bravais lattice vector
	0.0 1.0 0.0 second Bravais lattice vector		0.0 1.0 0.0 second Bravais lattice vector
Line 50:		Line 61:
	</pre>		</pre>

			Here's an example for Si C44 calculation, which will be changed later in PBS script every iteration.
	To do this calculation, you also need to put the LDA pseudopotential file as <tt>POTCAR</tt> in this directory.

	'''POSCAR example for C44'''

	<pre>		<pre>
	POSCAR for FCC Au		POSCAR for FCC Au
	4.~~062241~~ universal scaling factor		4.067877 universal scaling factor
	1.000 1.000 0.0 first lattice vector		1.000 1.000 0.0 first lattice vector
	-1.0 1.0 0.0 second lattice vector		-1.0 1.0 0.0 second lattice vector
Line 72:		Line 80:
	0.7500 0.2500 0.5000 T T T		0.7500 0.2500 0.5000 T T T
	</pre>		</pre>

			'''POTCAR'''

			In this example, we currently choose the US-LDA PP of Au provided by VASP. We will provide results of simulations with Au PAW-LDA PP in the later section.

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

Adrianos: /* Run VASP */

2015-08-26T11:09:51Z

Run VASP

← Older revision		Revision as of 11:09, 26 August 2015
Line 75:		Line 75:
	===Run VASP===		===Run VASP===

	To compute the elastic constants we use the following script <tt>auto.B.serial</tt> to run <tt>vasp</tt> repeated with different values for the first C11 component of the first Bravais lattice vector, '''$a'''. Make sure you have previously calculated the equilibrium lattice constant for this supercell with 4 atoms, otherwise errors in the calculations could arise. The script creates automatically the POSCAR file as in the example above for every '''a''' especified in the script in the range from 0.997 to 1.003		To compute the elastic constants we use the following script <tt>auto.B.serial</tt> to run <tt>vasp</tt> repeated with different values for the first C11 component of the first Bravais lattice vector, '''$a'''. Make sure you have previously calculated the equilibrium lattice constant for this supercell with 4 atoms, otherwise errors in the calculations could arise. The script creates automatically the POSCAR file as in the example above for every '''a''' especified in the script in the range from 0.997 to 1.003. For C44 script the $a value is changed for the first and the second components of the first Bravais lattice vector.

	'''Script for C11'''		'''Script for C11'''

Adrianos: /* Input files */

2015-08-26T07:57:25Z

Input files

← Older revision		Revision as of 07:57, 26 August 2015
Line 44:		Line 44:
	selective dynamics		selective dynamics
	direct direct or cart (only first letter is significant)		direct direct or cart (only first letter is significant)
	0.~~00000~~ 0.~~00000~~ 0.~~00000~~ T T T		0.0000 0.0000 0.0000 T T T
	0.~~50000~~ 0.~~50000~~ 0.~~00000~~ T T T		0.5000 0.5000 0.0000 T T T
	0.~~00000~~ 0.~~50000~~ 0.~~50000~~ T T T		0.0000 0.5000 0.5000 T T T
	0.~~50000~~ 0.~~00000~~ 0.~~50000~~ T T T		0.5000 0.0000 0.5000 T T T
	</pre>		</pre>

Adrianos: /* Run VASP */

2015-08-26T07:56:29Z

Run VASP

← Older revision		Revision as of 07:56, 26 August 2015
Line 86:		Line 86:
	cat > POSCAR << FIN		cat > POSCAR << FIN
	POSCAR for FCC Au		POSCAR for FCC Au
	4.062241 ~~from acurate VASP~~ lattice ~~calculation~~		4.062241 accurate equilibrium lattice constant
	$a 0.0 0.0 first Bravais lattice vector		$a 0.0 0.0 first Bravais lattice vector
	0.0 1.0 0.0 second Bravais lattice vector		0.0 1.0 0.0 second Bravais lattice vector
Line 93:		Line 93:
	selective dynamics		selective dynamics
	direct direct or cart (only first letter is significant)		direct direct or cart (only first letter is significant)
	0.~~00000~~ 0.~~00000~~ 0.~~00000~~ T T T		0.0000 0.0000 0.0000 T T T
	0.~~50000~~ 0.~~50000~~ 0.~~00000~~ T T T		0.5000 0.5000 0.0000 T T T
	0.~~00000~~ 0.~~50000~~ 0.~~50000~~ T T T		0.0000 0.5000 0.5000 T T T
	0.~~50000~~ 0.~~00000~~ 0.~~50000~~ T T T		0.5000 0.0000 0.5000 T T T
	FIN		FIN

Line 120:		Line 120:
	cat > POSCAR << FIN		cat > POSCAR << FIN
	POSCAR for FCC Au		POSCAR for FCC Au
	4.062241 ~~universal~~ ~~scaling~~ ~~factor~~		4.062241 accurate equilibrium lattice constant
	$a $a 0.0 first lattice vector		$a $a 0.0 first lattice vector
	-1.0 1.0 0.0 second lattice vector		-1.0 1.0 0.0 second lattice vector
	0.0 0.0 1.0 third lattice vector		0.0 0.0 1.0 third lattice vector
	8 number of atoms per species		8 number of atoms per species
	selective dynamics		selective dynamics
	direct direct or cart (only first letter is significant)		direct direct or cart (only first letter is significant)
	0 0.5000 0 T T T		0.0000 0.5000 0.0000 T T T
	0.2500 0.7500 0.5000 T T T		0.2500 0.7500 0.5000 T T T
	0 0 0 T T T		0.0000 0.0000 0.0000 T T T
	0.5000 0 0 T T T		0.5000 0.0000 0.0000 T T T
	0.2500 0.2500 0.5000 T T T		0.2500 0.2500 0.5000 T T T
	0.5000 0.5000 0 T T T		0.5000 0.5000 0.0000 T T T
	0.7500 0.7500 0.5000 T T T		0.7500 0.7500 0.5000 T T T
	0.7500 0.2500 0.5000 T T T		0.7500 0.2500 0.5000 T T T

Adrianos: /* Analyze data */

2015-08-26T07:50:29Z

Analyze data

← Older revision		Revision as of 07:50, 26 August 2015
Line 158:		Line 158:
	fit_C44EB('Elatt.C44.dat',a0,C11,C12);		fit_C44EB('Elatt.C44.dat',a0,C11,C12);

	In MATLAB click "~~add~~ ~~to path~~" when you open the file and ~~rmove~~ the semicolon to run it from the command line.		In MATLAB click "change folder" when you open the file and remove the semicolon to run it from the command line.
	The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively.		The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively.
	Refer to previous calculation?!)		Refer to previous calculation?!)
	The second ~~and third~~ lines ~~compute~~ the C11 and C12 elastic constants and the third line calculates C44. You ~~shuold~~ obtain C11= 213.0 GPa, C12= 179.2 GPa and C44= 40.4 GPa.		The second lines computes the C11 and C12 elastic constants and the third line calculates C44. You should obtain C11= 213.0 GPa, C12= 179.2 GPa and C44= 40.4 GPa.

	===Parallel computation===		===Parallel computation===

Adrianos: /* Analyze data */

2015-08-26T07:46:54Z

Analyze data

← Older revision		Revision as of 07:46, 26 August 2015
Line 157:		Line 157:
	fit_C11EB('Elatt.C11.dat',a0,B);		fit_C11EB('Elatt.C11.dat',a0,B);
	fit_C44EB('Elatt.C44.dat',a0,C11,C12);		fit_C44EB('Elatt.C44.dat',a0,C11,C12);


	In ~~MATALB~~ ~~remove~~ the ~~semicolon~~ and ~~click~~ the ~~add~~ to ~~path~~ ~~bottom~~.		In MATLAB click "add to path" when you open the file and rmove the semicolon to run it from the command line.
	The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively.		The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively.
	Refer to previous calculation?!)		Refer to previous calculation?!)

Adrianos: /* Analyze data */

2015-08-26T07:43:59Z

Analyze data

← Older revision		Revision as of 07:43, 26 August 2015
Line 150:		Line 150:
	===Analyze data===		===Analyze data===

	After running the two scripts above for C11 and C44 s <tt>./auto.B.serial</tt>, it will create data files: <tt>Elatt.C11.dat</tt> ~~and~~ <tt>platt.C11.dat</tt> <tt>Elatt.C44.dat</tt> and <tt>platt.C44.dat</tt>.		After running the two scripts above for C11 and C44, <tt>./auto.B.serial</tt> it will create the data files: <tt>Elatt.C11.dat</tt>,<tt>platt.C11.dat</tt>, <tt>Elatt.C44.dat</tt>, and <tt>platt.C44.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]], '''cal_VASP.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]], '''cal_VASP.m'''
	~~[a0, Ecoh, B] =~~ fit_a0EB('Elatt.B.dat',4,4);		fit_a0EB('Elatt.B.dat',4,4);
	~~[C11,C12] =~~ fit_C11EB('Elatt.C11.dat',a0,B);		fit_C11EB('Elatt.C11.dat',a0,B);
	~~C44 =~~ fit_C44EB('Elatt.C44.dat',a0,C11,C12);		fit_C44EB('Elatt.C44.dat',a0,C11,C12);

			In MATALB remove the semicolon and click the add to path bottom.
	The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus. (~~Refer~~ to ~~previous calculation?!~~)		The first line fits the energy data to a quadratic curve and computes the equilibrium lattice constant, cohesive energy and bulk modulus(['''a0, Ecoh, B]''') respectively.
			Refer to previous calculation?!)
	The second and third lines compute the C11 and C12 elastic constants and the third line calculates C44. You shuold obtain C11= 213.0 GPa, C12= 179.2 GPa and C44= 40.4 GPa.		The second and third lines compute the C11 and C12 elastic constants and the third line calculates C44. You shuold obtain C11= 213.0 GPa, C12= 179.2 GPa and C44= 40.4 GPa.