Shuffle-Glide dislocation MD and NEB - Revision history

Xzhang11 at 18:10, 13 March 2018

2018-03-13T18:10:46Z

← Older revision		Revision as of 18:10, 13 March 2018
Line 139:		Line 139:
	The third line needs to be launched within pbs file `cause it execute sworig_mc2_mpich in MPI mode, calling stringrelax_parallel (). The energy barrier curve can be visualized by using octave/matlab such as,		The third line needs to be launched within pbs file `cause it execute sworig_mc2_mpich in MPI mode, calling stringrelax_parallel (). The energy barrier curve can be visualized by using octave/matlab such as,

	===Test case 2: Energy barrier with SW for strain 0.~~0520~~===		===Test case 2: Energy barrier with SW for strain 5.2%===

	::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out		::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out
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	::> mpirun -np $ncpu lammps-30Jul16/src/lmp_mpi < input.meam		::> mpirun -np $ncpu lammps-30Jul16/src/lmp_mpi < input.meam

	===Test case 3: Nucleation event with SW for strain 0.~~0520~~===		===Test case 3: Nucleation event with SW for strain 5.2%===

	::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out		::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out

Xzhang11 at 18:09, 13 March 2018

2018-03-13T18:09:59Z

← Older revision		Revision as of 18:09, 13 March 2018
Line 180:		Line 180:

	===Test case 3: Nucleation event with SW for strain 0.0520===		===Test case 3: Nucleation event with SW for strain 0.0520===

			::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out
			::> plot(stringeng(1:100:end, 3:5:end)', '*')

			Apply this work flow for different strain, one gets the energy barrier as a function of applied strain.

Xzhang11 at 18:09, 13 March 2018

2018-03-13T18:09:16Z

← Older revision		Revision as of 18:09, 13 March 2018
Line 138:		Line 138:

	The third line needs to be launched within pbs file `cause it execute sworig_mc2_mpich in MPI mode, calling stringrelax_parallel (). The energy barrier curve can be visualized by using octave/matlab such as,		The third line needs to be launched within pbs file `cause it execute sworig_mc2_mpich in MPI mode, calling stringrelax_parallel (). The energy barrier curve can be visualized by using octave/matlab such as,

			===Test case 2: Energy barrier with SW for strain 0.0520===

	::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out		::> load runs/he-si-tf-pit-neb/he-si-tf-pit-special-3-sworig/w-disl-nuc-hetero-001-0.0520.24/stringeng.out
Line 146:		Line 148:
	Note that, dislocation loop size of status == 1 can be adjusted manually in the script by specifying w in make_glide_dislocation_loop_1, for example, minor adjustment is needed to get a smooth energy barrier - strain curve.		Note that, dislocation loop size of status == 1 can be adjusted manually in the script by specifying w in make_glide_dislocation_loop_1, for example, minor adjustment is needed to get a smooth energy barrier - strain curve.


	==Benchmark in Lammps==
			==Finite temperature MD with Lammps==

	We use lammps-30Jul16 version.		We use lammps-30Jul16 version.
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	::> cd MD++.git/scripts/work/he-si-tf-pit-md/he-si-pit-800K-54-thermal-relax-nvt		::> cd MD++.git/scripts/work/he-si-tf-pit-md/he-si-pit-800K-54-thermal-relax-nvt
	::> mpirun -np $ncpu lammps-30Jul16/src/lmp_mpi < input.meam		::> mpirun -np $ncpu lammps-30Jul16/src/lmp_mpi < input.meam

			===Test case 3: Nucleation event with SW for strain 0.0520===

Xzhang11 at 18:01, 13 March 2018

2018-03-13T18:01:25Z

← Older revision		Revision as of 18:01, 13 March 2018
Line 5:		Line 5:
	<P ALIGN="CENTER"><STRONG>Xiaohan Zhang and Wei Cai</STRONG></P>		<P ALIGN="CENTER"><STRONG>Xiaohan Zhang and Wei Cai</STRONG></P>
	</DIV>		</DIV>
	<P ALIGN="CENTER"> Created Mar, ~~2017~~, Last modified Mar, ~~2017~~</P>		<P ALIGN="CENTER"> Created Mar, 2018, Last modified Mar, 2018</P>
	<P>		<P>

Xzhang11: /* Benchmark in Lammps */

2018-03-12T22:53:52Z

Benchmark in Lammps

← Older revision		Revision as of 22:53, 12 March 2018
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	We use lammps-30Jul16 version.		We use lammps-30Jul16 version.

	::> cd ~~/home/xzhang11/Planet/Codes/~~lammps-30Jul16/lib/meam		::> cd lammps-30Jul16/lib/meam
	::> make -f Makefile.gfortran (for meam)		::> make -f Makefile.gfortran (for meam)
	::> cd ~~/home/xzhang11/Planet/Codes/~~lammps-30Jul16/src		::> cd lammps-30Jul16/src
	::> make yes-manybody		::> make yes-manybody
	::> make yes-meam		::> make yes-meam
	::> make mpi		::> make mpi


			First, one estimates thermal expansion ratios for a bulk system of si using MEAM and sworig.

			::> cd MD++.git/
			::> bin1/sworig_mc2 scripts/work/he-si-tf-pit-md/thermal_init_config/therm_exp_estimates/bulk_generator.tcl 0
			::> cd /home/xzhang11/Planet/Libs/MD++.git/scripts/work/he-si-tf-pit-
			md/thermal_init_config/therm_exp_estimates/thermal_equilibrate_load_hold_si_800K
			::> lmp_mpi < thermal_equilibrate.sw (meam)

			From initial and final equilibrated states, one gets thermal expansion. And one records the coefficents in
			scripts/work/he-si-tf-pit-md/thermal_init_config/therm_initconfig_generator.tcl

			::> sw_mc2 scripts/work/he-si-tf-pit-md/thermal_init_config/therm_initconfig_generator.tcl 0 1 1000

	To run the lammps scripts, first create surface pit structure with MD++ as follows,		To run the lammps scripts, first create surface pit structure with MD++ as follows,

			::> cd MD++.git/scripts/work/he-si-tf-pit-md/he-si-pit-800K-54-thermal-relax-nvt
			::> mpirun -np $ncpu lammps-30Jul16/src/lmp_mpi < input.meam

Xzhang11: /* Benchmark in MD++ */

2018-03-12T20:59:44Z

Benchmark in MD++

← Older revision		Revision as of 20:59, 12 March 2018
Line 146:		Line 146:
	Note that, dislocation loop size of status == 1 can be adjusted manually in the script by specifying w in make_glide_dislocation_loop_1, for example, minor adjustment is needed to get a smooth energy barrier - strain curve.		Note that, dislocation loop size of status == 1 can be adjusted manually in the script by specifying w in make_glide_dislocation_loop_1, for example, minor adjustment is needed to get a smooth energy barrier - strain curve.

	==Benchmark in ~~MD++~~==		==Benchmark in Lammps==

			We use lammps-30Jul16 version.
	Compile the code using the following command on mc2.

			::> cd /home/xzhang11/Planet/Codes/lammps-30Jul16/lib/meam
	make meam-lammps build=R SYS=mc2_mpich
			::> make -f Makefile.gfortran (for meam)
			::> cd /home/xzhang11/Planet/Codes/lammps-30Jul16/src
			::> make yes-manybody
			::> make yes-meam
			::> make mpi

	Use the following command to compute the melting point of pure Si, Ge, and Si0.5Ge0.5.

			To run the lammps scripts, first create surface pit structure with MD++ as follows,
	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 1

	The results are

	a0 = 4.07300759775 Angstrom
	Ecoh = -3.92996804082 eV

	Use the following command to compute the equilibrium lattice constant and cohesive energy of pure Si (DC).

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 0

	The results are

	a0 = 5.43100051581 Angstrom
	Ecoh = -4.63000000205 eV


	Use the following command to compute the equilibrium lattice constant and cohesive energy of Au-Si (B1).

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 2

	The results are

	a0 = 5.4 Angstrom
	Ecoh = -4.155000000083061 eV

	===melting point===

	Use the following command to compute the impurity of a Au atom in Si DC lattice.

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 4

	The results depend slightly on the cell size
	cell size, Eimp(eV)
	3x3x3 3.914
	4x4x4 3.968
	5x5x5 3.987
	10x10x10 4.005
	20x20x20 4.008

	The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
	is <math>E_2 = 3.968</math> (eV) for a Au atom in Si DC crystal.
	So it seems that the result in JPCM (2010) corresponds to the 4x4x4 cell here.


	Use the following command to compute the impurity of a Si atom in Au fcc lattice.

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 3

	cell size, Eimp(eV)
	2x2x2 0.639
	3x3x3 0.660
	4x4x4 0.665
	5x5x5 0.667
	10x10x10 0.669
	20x20x20 0.669

	The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
	is <math>E_1 = 0.636</math> (eV) for a Si atom in Au FCC crystal.
	So it seems that for a Si in Au FCC crystal, the predicted results here using
	the 2x2x2 cell corresponds to the value in JPCM (2010).

	===phase diagram===

	Use the following command to obtain the phase diagram of SiGe.

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 4

	The results depend slightly on the cell size
	cell size, Eimp(eV)
	3x3x3 3.914
	4x4x4 3.968
	5x5x5 3.987
	10x10x10 4.005
	20x20x20 4.008

	The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
	is <math>E_2 = 3.968</math> (eV) for a Au atom in Si DC crystal.
	So it seems that the result in JPCM (2010) corresponds to the 4x4x4 cell here.


	Use the following command to compute the impurity of a Si atom in Au fcc lattice.

	bin/meam-lammps_gpp scripts/work/si_au/si_au_benchmark.tcl 3

	cell size, Eimp(eV)
	2x2x2 0.639
	3x3x3 0.660
	4x4x4 0.665
	5x5x5 0.667
	10x10x10 0.669
	20x20x20 0.669

	The result in the paper (S. Ryu and W.Cai JPCM 22 055401 (2010), Table 2,
	is <math>E_1 = 0.636</math> (eV) for a Si atom in Au FCC crystal.
	So it seems that for a Si in Au FCC crystal, the predicted results here using
	the 2x2x2 cell corresponds to the value in JPCM (2010).

Xzhang11: /* NEB calculation work flow */

2018-03-12T20:54:00Z

NEB calculation work flow

← Older revision		Revision as of 20:54, 12 March 2018
Line 143:		Line 143:

	Apply this work flow for different strain, one gets the energy barrier as a function of applied strain.		Apply this work flow for different strain, one gets the energy barrier as a function of applied strain.

			Note that, dislocation loop size of status == 1 can be adjusted manually in the script by specifying w in make_glide_dislocation_loop_1, for example, minor adjustment is needed to get a smooth energy barrier - strain curve.

	==Benchmark in MD++==		==Benchmark in MD++==

Xzhang11: /* NEB calculation work flow */

2018-03-12T20:51:52Z

NEB calculation work flow

@@ Line 125: / Line 125: @@
 ) null                       2) intel/14                   3) mvapich2/2.0rc1-intel-14
       ::> make sworig build=R SYS=mc2_mpich
 ==Benchmark in MD++==

Xzhang11: /* Cross Potential between Ge and Si */

2018-03-12T20:43:58Z

Cross Potential between Ge and Si

← Older revision		Revision as of 20:43, 12 March 2018
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	SW + SiGeHole_sw.cn : -996031.74		SW + SiGeHole_sw.cn : -996031.74

			==NEB calculation work flow==
	==Cross Potential between Ge and Si==

			::> cd MD++.git
	The parameters for the cross potential are specified in '''SiGe.meam''' file. The lines relevant for the cross potential (i.e. between species 1 and 2) are shown below. The values correspond to Table 1 of G. Grochola et al. / Chemical Physics Letters 493 (2010) 57–60 59.
			::> module list

			Currently Loaded Modulefiles:
	re(1,2) = 2.67 (<math>r_e</math>)
			1) null 2) intel/14 3) mvapich2/2.0rc1-intel-14
	delta(1,2) = 0.071 (related to <math>E_c</math>, see below)
			::> make sworig build=R SYS=mc2_mpich
	lattce(1,2) = b1 (<math>B</math>)
	lattce(1,2) = b1 (<math>Rcut</math>)
	lattce(1,2) = b1 (<math>C_{\max}</math>)
	lattce(1,2) = b1 (<math>C_{\min}</math>)
	d = 0

	The values for <math>E_c ({\rm AuGe}) = 3.189</math>.
	This value is related to delta(1,2) through

	<math>E_c ({\rm AuGe}) = 0.5[ E_c ({\rm Au}) + E_c({\rm Ge}) ] - {\rm delta}(1,2) = 0.5 (3.93 + 3.85) - 0.071 = 3.819</math>.

	<math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> = 1.5228 because of the <math>\rho_0^{\rm Ge}</math> and <math>\rho_0^{\rm Au}</math> values specified above. This value of <math>\rho_0^{\rm Ge} / \rho_0^{\rm Au}</math> leads to the following impurity formation energies

	<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (MEAM)
	<math>E_2 = 1.387 </math> eV Au impurity in DC Ge (MEAM)

	These values are to be compared with VASP predictions

	<math>E_1 = 0.331 </math> eV Ge impurity in FCC Au (VASP/LDA/US)
	<math>E_2 = 1.130 </math> eV Au impurity in DC Ge (VASP/LDA/US)

	Cmax = 2.8 is the default value.

	==Benchmark in MD++==		==Benchmark in MD++==

Xzhang11: /* Test case 1: Potential Calibration for SW and MEAM */

2018-03-12T20:41:39Z

Test case 1: Potential Calibration for SW and MEAM

← Older revision		Revision as of 20:41, 12 March 2018
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	::> meam-lammps_mc2 scripts/work/sw_meam_calibrations/disl_nuc_hetero.tcl 1 0 1000		::> meam-lammps_mc2 scripts/work/sw_meam_calibrations/disl_nuc_hetero.tcl 1 0 1000

	change in the script the configuration to read in, choosing from runs/sw_meam_calibrations/bulk_sw.cn, ~~bulk_meam~~.cn, ~~SiGeHole_meam~~.cn, ~~SiGeHole_sw~~.cn. ~~From~~ ~~MD++,~~ ~~the numbers should be exactly~~ ~~the~~ ~~following:~~		change in the script the configuration to read in, choosing from runs/sw_meam_calibrations/bulk_sw.cn, SiGeHole_sw.cn. (There are also bulk_meam.cn, SiGeHole_meam.cn generated from disl_nuc_hetero.tcl with meam-lammps)

			From MD++, the numbers should be exactly the following:

	MEAM + bulk_sw.cn : -1.024081.9		MEAM + bulk_sw.cn : -1.024081.9