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.

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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 $R_{i}^{0}$ = alat 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 \times \sqrt{3}/4} for the diamond cubic structure.

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 \rho_0^{\rm Si}} = 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, bulk_meam.cn, SiGeHole_meam.cn, SiGeHole_sw.cn. From MD++, the numbers should be exactly the following:

MEAM + bulk_meam.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

Cross Potential between Ge and Si

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.

re(1,2) = 2.67         ($r_{e}$)
delta(1,2) = 0.071      (related to $E_{c}$, see below)
lattce(1,2) = b1         ($B$)
lattce(1,2) = b1         ($Rcut$)
lattce(1,2) = b1         ($C_{\max }$)
lattce(1,2) = b1         ($C_{\min }$)
d = 0 

The values for $E_{c}({\rm {AuGe}})=3.189$. This value is related to delta(1,2) through

$E_{c}({\rm {AuGe}})=0.5*[E_{c}({\rm {Au}})+E_{c}({\rm {Ge}})]-{\rm {delta}}(1,2)=0.5*(3.93+3.85)-0.071=3.819$.

$\rho _{0}^{\rm {Ge}}/\rho _{0}^{\rm {Au}}$ = 1.5228 because of the $\rho _{0}^{\rm {Ge}}$ and $\rho _{0}^{\rm {Au}}$ values specified above. This value of $\rho _{0}^{\rm {Ge}}/\rho _{0}^{\rm {Au}}$ leads to the following impurity formation energies

$E_{1}=0.331$ eV   Ge impurity in FCC Au (MEAM)
$E_{2}=1.387$ eV   Au impurity in DC  Ge (MEAM)

These values are to be compared with VASP predictions

$E_{1}=0.331$ eV   Ge impurity in FCC Au (VASP/LDA/US)
$E_{2}=1.130$ eV   Au impurity in DC  Ge (VASP/LDA/US)

Cmax = 2.8 is the default value.

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 $E_{2}=3.968$ (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 $E_{1}=0.636$ (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 $E_{2}=3.968$ (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 $E_{1}=0.636$ (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).