Shuffle-Glide dislocation MD and NEB
Shuffle Glide Dislocation Complex: NEB and MD
Xiaohan Zhang and Wei Cai
Created Mar, 2017, Last modified Mar, 2017
This tutorial corresponds to paper ``Shuffle-Glide Dislocation Complex Nucleation in Silicon Thin Film. It explains how to calibrate and specify SW and MEAM-lammps potential parameters in both MD++ and LAMMPs. It explains how to set up and run NEB calculations to measure the energy barrier of a shuffle-glide dislocation complex nucleated in a thin film with a surface pit. Finite temperature MD simulations are performed in Lammps to capture nucleation events as validation to energy barrier calculations.
Potential for Pure Elements
SW Potential for Si
We calibrate both SW (1985) and SW (1992) potentials in both MD++ and Lammps. The modified version of SW fits to cohesive energy. Their parameters are listed as follows:
MD++: /* original Si version PRB 31, 5262 (1985) */
aa=15.27991323; bb=11.60319228; plam=45.51575;
pgam=2.51412; acut=3.77118; pss=2.0951; rho=4.0;
/* modified Si parameters PRB 46, 2250 (1992) */
aa=16.31972277; bb=11.60319228; plam=48.61499998;
pgam=2.51412; acut=3.77118; pss=2.0951; rho=4.;
Lammps:
/* sw, Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985) */
Si Si Si 2.1674166667 2.0951 1.80 21.0 1.20 -0.333333333
7.049827 0.602225 4.0 0.0 0.0
/* PRB 46, 2250 (1992) */
Si Si Si 2.1683 2.0951 1.80 22.4207904718 1.20 -0.333333333333
7.5265059125 0.6022245574 4.0 0.0 0.0
MEAM Potential for Si
We use the 'Siz' potential as those used in Kang, et al "Size and Temperature Effects on Brittle and Ductile Fracture of Silicon Nanowires", International Journal of Plasticity, 26, 1387 (2010" and "Brittle and Ductile Fracture of Semiconductor Nanowires – Molecular Dynamics Simulations", Philosophical Magazine, 87, 2169, (2007)."
MD++:
The main parameters in the MEAM potential is specified in the meamf file. (In MD++, this file is in the potentials/MEAMDATA folder.) The lines correspond to 'Siz' is given below.
'Siz' 'dia' 4. 14 28.086
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.
1.0 3.13 4.47 -1.80 1.600 0
corresponding to the data format of:
elt lat z ielement atwt
alpha b0 b1 b2 b3 alat esub asub
t0 t1 t2 t3 rozero ibar
Note that the nearest neighbor distance = alat for the diamond cubic structure.
= rozero will be important only for cross-potential. And note that this is the only different from Si4 line.
ibar is a setting used in the equation of state (EOS), which is explained in SiGe potential tutorial (http://micro.stanford.edu/wiki/MEAM_Potential_for_Si-Ge)
Lammps:
'Siz' 'dia' 4. 14 28.086
4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.
1.0 3.13 4.47 -1.80 1.600 0
corresponds to the data format of
DATE: 2012-06-29 DATE: 2007-06-11 CONTRIBUTOR:
Greg Wagner, gjwagne@sandia.gov
CITATION: Baskes, Phys Rev B, 46, 2727-2742 (1992)
meam data from vax files fcc,bcc,dia 11/4/92
elt lat z ielement atwt
alpha b0 b1 b2 b3 alat esub asub
t0 t1 t2 t3 rozero ibar
Test case 1: Potential Calibration for SW and MEAM
This test case is developed in MD++, but also use lammps executable, to evaluate potential energy of a bulk system and a surface pit structure with both SW (1985, 1992) and MEAM potential. To run the test case, follow the steps below,
Take mc2 as an example, one module load the following:
::> module load mvapich2/2.0rc1-intel-14, intel/14
::> cd MD++.git (svn)
::> make sworig build=R SYS=mc2_mpich
::> make sw build=R SYS=mc2_mpich
::> make meam-lammps build=R SYS=mc2
::> bin1/sworig_mc2_mpich scripts/work/sw_meam_calibrations/disl_nuc_hetero.tcl 1 0 1000
(0 and 1000 are useless, but need to be there otherwise the script will complain missing parameters)
::> bin1/sw_mc2_mpich 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, 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 + SiGeHole_sw.cn: -9.97015.8
SWorig + bulk_sw.cn : -9.58832.6
SWorig + SiGeHole_sw.cn : -9.32569.7
SW + bulk_sw.cn : -1.024081.9
SW + SiGeHole_sw.cn : -9.96031.739
From lammps,
MEAM + bulk_sw.cn : -1024081.9
MEAM + SiGeHole_sw.cn: -997015.9
SWorig + bulk_sw.cn : -958832.17
SWorig + SiGeHole_sw.cn : -932569.26
SW + bulk_sw.cn : -1024081.9
SW + SiGeHole_sw.cn : -996031.74
NEB calculation work flow
::> cd MD++.git
::> module list
Currently Loaded Modulefiles:
1) null 2) intel/14 3) mvapich2/2.0rc1-intel-14
::> make sworig build=R SYS=mc2_mpich
Benchmark in MD++
Compile the code using the following command on mc2.
make meam-lammps build=R SYS=mc2_mpich
Use the following command to compute the melting point of pure Si, Ge, and Si0.5Ge0.5.
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 (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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle E_1 = 0.636} (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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle E_2 = 3.968} (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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle E_1 = 0.636} (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).