Removed compute*.dat and *v2 files
This commit is contained in:
Pedro Antonio Santos Flórez
@ -1,17 +0,0 @@
|
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# Time-averaged data for fix snap
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43]
|
||||
0 13
|
||||
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87
|
||||
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188
|
||||
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829
|
||||
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128
|
||||
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188
|
||||
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829
|
||||
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128
|
||||
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08
|
||||
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08
|
||||
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08
|
||||
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06
|
||||
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06
|
||||
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06
|
||||
@ -1,17 +0,0 @@
|
||||
# Time-averaged data for fix snap
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43]
|
||||
0 13
|
||||
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87
|
||||
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188
|
||||
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829
|
||||
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128
|
||||
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188
|
||||
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829
|
||||
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128
|
||||
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08
|
||||
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08
|
||||
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08
|
||||
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06
|
||||
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06
|
||||
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06
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||||
@ -1,17 +0,0 @@
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# Time-averaged data for fix snap
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# TimeStep Number-of-rows
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# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13]
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||||
0 13
|
||||
1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87
|
||||
2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188
|
||||
3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829
|
||||
4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128
|
||||
5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188
|
||||
6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829
|
||||
7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128
|
||||
8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08
|
||||
9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08
|
||||
10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08
|
||||
11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06
|
||||
12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06
|
||||
13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06
|
||||
@ -1,17 +0,0 @@
|
||||
# Time-averaged data for fix snap
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13]
|
||||
0 13
|
||||
1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87
|
||||
2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188
|
||||
3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829
|
||||
4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128
|
||||
5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188
|
||||
6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829
|
||||
7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128
|
||||
8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08
|
||||
9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08
|
||||
10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08
|
||||
11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06
|
||||
12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06
|
||||
13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06
|
||||
@ -1,156 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Demonstrate MLIAP interface to linear SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.3160000 3.3160000 3.3160000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000 13.264000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.mliap
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
|
||||
# Specify hybrid with SNAP, ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model linear Ta06A.mliap.model descriptor sna Ta06A.mliap.descriptor
|
||||
Reading potential file Ta06A.mliap.model with DATE: 2014-09-05
|
||||
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
|
||||
SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword nelems 1
|
||||
SNAP keyword elems Ta
|
||||
SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * mliap Ta
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8
|
||||
ghost atom cutoff = 5.8
|
||||
binsize = 2.9, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.15 | 18.15 | 18.15 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661
|
||||
10 296.01467 -11.851059 -11.851059 -11.813095 2697.4796 -2697.4796
|
||||
20 284.53666 -11.849587 -11.849587 -11.813095 2289.1527 -2289.1527
|
||||
30 266.51577 -11.847275 -11.847275 -11.813095 1851.7131 -1851.7131
|
||||
40 243.05007 -11.844266 -11.844266 -11.813095 1570.684 -1570.684
|
||||
50 215.51032 -11.840734 -11.840734 -11.813094 1468.1899 -1468.1899
|
||||
60 185.48331 -11.836883 -11.836883 -11.813094 1524.8757 -1524.8757
|
||||
70 154.6736 -11.832931 -11.832931 -11.813094 1698.3351 -1698.3351
|
||||
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
|
||||
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
|
||||
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
|
||||
Loop time of 1.80936 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.388 ns/day, 10.052 hours/ns, 55.268 timesteps/s
|
||||
80.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.8055 | 1.8055 | 1.8055 | 0.0 | 99.78
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00133 | 0.00133 | 0.00133 | 0.0 | 0.07
|
||||
Output | 0.001145 | 0.001145 | 0.001145 | 0.0 | 0.06
|
||||
Modify | 0.000669 | 0.000669 | 0.000669 | 0.0 | 0.04
|
||||
Other | | 0.000749 | | | 0.04
|
||||
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727.000 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3712.00 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424.00 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,167 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Demonstrate MLIAP interface to SNAP W-Be potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803000 3.1803000 3.1803000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (12.721200 12.721200 12.721200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 183.84
|
||||
mass 2 9.012182
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
Setting atom values ...
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group beryllium type 2
|
||||
5 atoms in group beryllium
|
||||
# choose potential
|
||||
|
||||
include WBe_Wood_PRB2019.mliap
|
||||
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz1 equal 74
|
||||
variable zblz2 equal 4
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model linear WBe_Wood_PRB2019.mliap.model descriptor sna WBe_Wood_PRB2019.mliap.descriptor
|
||||
Reading potential file WBe_Wood_PRB2019.mliap.model with DATE: 2019-09-18
|
||||
Reading potential file WBe_Wood_PRB2019.mliap.descriptor with DATE: 2019-09-18
|
||||
SNAP keyword rcutfac 4.8123
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems W
|
||||
SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 1
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 1 zbl 74 ${zblz1}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 1 2 zbl 74 ${zblz2}
|
||||
pair_coeff 1 2 zbl 74 4
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff 2 2 zbl 4 ${zblz2}
|
||||
pair_coeff 2 2 zbl 4 4
|
||||
pair_coeff * * mliap W Be
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8123
|
||||
ghost atom cutoff = 5.8123
|
||||
binsize = 2.90615, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 48.80 | 48.80 | 48.80 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -8.5980876 -8.5980876 -8.5596125 -35284.855 35284.855
|
||||
10 296.32664 -8.5976164 -8.5976164 -8.5596124 -35188.339 35188.339
|
||||
20 282.41417 -8.595832 -8.595832 -8.5596123 -34782.293 34782.293
|
||||
30 259.69014 -8.5929175 -8.5929175 -8.5596121 -34113.316 34113.316
|
||||
40 230.50415 -8.5891741 -8.5891741 -8.5596119 -33260.777 33260.777
|
||||
50 197.88816 -8.5849908 -8.5849908 -8.5596116 -32309.975 32309.975
|
||||
60 165.27259 -8.5808076 -8.5808076 -8.5596113 -31365.766 31365.766
|
||||
70 136.15697 -8.5770733 -8.5770733 -8.5596111 -30542.657 30542.657
|
||||
80 113.58947 -8.5741788 -8.5741788 -8.5596109 -29939.23 29939.23
|
||||
90 99.477916 -8.572369 -8.572369 -8.5596109 -29619.939 29619.939
|
||||
100 94.121939 -8.5716822 -8.5716822 -8.559611 -29598.002 29598.002
|
||||
Loop time of 5.14269 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.840 ns/day, 28.570 hours/ns, 19.445 timesteps/s
|
||||
82.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1376 | 5.1376 | 5.1376 | 0.0 | 99.90
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.001657 | 0.001657 | 0.001657 | 0.0 | 0.03
|
||||
Output | 0.002107 | 0.002107 | 0.002107 | 0.0 | 0.04
|
||||
Modify | 0.00052 | 0.00052 | 0.00052 | 0.0 | 0.01
|
||||
Other | | 0.00078 | | | 0.02
|
||||
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727.000 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3712.00 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424.00 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Demonstrate MLIAP interface to ChemSNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 5.83
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond $a
|
||||
lattice diamond 5.83
|
||||
Lattice spacing in x,y,z = 5.8300000 5.8300000 5.8300000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (23.320000 23.320000 23.320000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
|
||||
Created 512 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# choose potential
|
||||
|
||||
include InP_JCPA2020.mliap
|
||||
# DATE: 2020-06-01 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
|
||||
variable zblcutinner index 4
|
||||
variable zblcutouter index 4.2
|
||||
variable zblz1 index 49
|
||||
variable zblz2 index 15
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.2 mliap model linear InP_JCPA2020.mliap.model descriptor sna InP_JCPA2020.mliap.descriptor
|
||||
Reading potential file InP_JCPA2020.mliap.model with DATE: 2020-06-01
|
||||
Reading potential file InP_JCPA2020.mliap.descriptor with DATE: 2020-06-01
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems In
|
||||
SNAP keyword radelems 3.81205
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0.0
|
||||
SNAP keyword bzeroflag 1
|
||||
SNAP keyword wselfallflag 1
|
||||
SNAP keyword chemflag 1
|
||||
SNAP keyword bnormflag 1
|
||||
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 ${zblz1}
|
||||
pair_coeff 1 1 zbl 49 49
|
||||
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 ${zblz2}
|
||||
pair_coeff 1 2 zbl 49 15
|
||||
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 ${zblz2}
|
||||
pair_coeff 2 2 zbl 15 15
|
||||
pair_coeff * * mliap In P
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.6589
|
||||
ghost atom cutoff = 8.6589
|
||||
binsize = 4.32945, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 187.1 | 187.1 | 187.1 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -3.4805794 0 -3.4418771 1353.5968
|
||||
10 285.84677 -3.4787531 0 -3.4418766 1611.7131
|
||||
20 248.14649 -3.4738884 0 -3.4418756 2312.0308
|
||||
30 198.94136 -3.4675394 0 -3.4418744 3168.1543
|
||||
40 152.74831 -3.4615791 0 -3.4418734 3903.5749
|
||||
50 121.9796 -3.4576091 0 -3.4418728 4387.1254
|
||||
60 113.27555 -3.4564863 0 -3.4418729 4556.3003
|
||||
70 125.68089 -3.4580873 0 -3.4418735 4431.2083
|
||||
80 151.47475 -3.4614159 0 -3.4418745 4107.2369
|
||||
90 179.18708 -3.4649919 0 -3.4418754 3739.5881
|
||||
100 197.50662 -3.4673559 0 -3.441876 3492.7778
|
||||
Loop time of 24.0349 on 1 procs for 100 steps with 512 atoms
|
||||
|
||||
Performance: 0.180 ns/day, 133.527 hours/ns, 4.161 timesteps/s
|
||||
92.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 24.031 | 24.031 | 24.031 | 0.0 | 99.99
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.001691 | 0.001691 | 0.001691 | 0.0 | 0.01
|
||||
Output | 0.00034 | 0.00034 | 0.00034 | 0.0 | 0.00
|
||||
Modify | 0.00082 | 0.00082 | 0.00082 | 0.0 | 0.00
|
||||
Other | | 0.000746 | | | 0.00
|
||||
|
||||
Nlocal: 512.000 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1959.00 ave 1959 max 1959 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31232.0 ave 31232 max 31232 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 62464.0 ave 62464 max 62464 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 62464
|
||||
Ave neighs/atom = 122.00000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:24
|
||||
@ -1,282 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2.0000000 2.0000000 2.0000000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (2.0000000 2.0000000 2.0000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
Displacing atoms ...
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 0
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
# run compute mliap with gradgradflag = 1
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 1
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg1.dat mode vector
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.75 | 10.75 | 10.75 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
200.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2.00000 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853.000 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330.000 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660.000 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330.00000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
uncompute snap
|
||||
unfix snap
|
||||
|
||||
# run compute mliap with gradgradflag = 0
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear gradgradflag 0
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.gg0.dat mode vector
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:691)
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.89 | 22.89 | 22.89 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2.00000 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853.000 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330.000 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660.000 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330.00000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,282 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Demonstrate MLIAP quadratic compute
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2.0000000 2.0000000 2.0000000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (2.0000000 2.0000000 2.0000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
Displacing atoms ...
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 1
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_100 equal c_db[2][100]
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
thermo 100
|
||||
|
||||
# run compute mliap with gradgradflag = 1
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 1
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg1.dat mode vector
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.47 | 22.47 | 22.47 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
200.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2.00000 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853.000 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330.000 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660.000 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330.00000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
uncompute snap
|
||||
unfix snap
|
||||
|
||||
# run compute mliap with gradgradflag = 0
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic gradgradflag 0
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.gg0.dat mode vector
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:691)
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 70.24 | 70.24 | 70.24 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2.00000 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853.000 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330.000 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660.000 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330.00000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
|
||||
# Demonstrate MLIAP interface to quadratic SNAP potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803000 3.1803000 3.1803000
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (12.721200 12.721200 12.721200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
displace_atoms all random 0.01 0.01 0.01 12345
|
||||
Displacing atoms ...
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
# choose potential
|
||||
|
||||
include W.quadratic.mliap
|
||||
# DATE: 2020-06-21 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: none
|
||||
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 74
|
||||
|
||||
# Specify hybrid with SNAP and ZBL
|
||||
|
||||
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
||||
pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor
|
||||
Reading potential file W.quadratic.mliap.model with DATE: 2020-06-21
|
||||
Reading potential file W.quadratic.mliap.model with DATE: 2020-06-21
|
||||
Reading potential file W.quadratic.mliap.descriptor with DATE: 2020-06-21
|
||||
SNAP keyword rcutfac 4.73442
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword nelems 1
|
||||
SNAP keyword elems W
|
||||
SNAP keyword radelems 0.5
|
||||
SNAP keyword welems 1
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 1
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 74 ${zblz}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff * * mliap W
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
compute eatom all pe/atom
|
||||
compute energy all reduce sum c_eatom
|
||||
|
||||
compute satom all stress/atom NULL
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp epair c_energy etotal press v_press
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
|
||||
timestep 0.5e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify once no every 1 delay 0 check no
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.8
|
||||
ghost atom cutoff = 5.8
|
||||
binsize = 2.9, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair zbl, perpetual, half/full from (2)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair mliap, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 192.1 | 192.1 | 192.1 Mbytes
|
||||
Step Temp E_pair c_energy TotEng Press v_press
|
||||
0 300 -1.1602728 -1.1602728 -1.1217977 600047.3 -600047.3
|
||||
10 288.46387 -1.1587932 -1.1587932 -1.1217976 600359.75 -600359.75
|
||||
20 268.69718 -1.1562579 -1.1562579 -1.1217974 600870.22 -600870.22
|
||||
30 243.19855 -1.1529874 -1.1529874 -1.1217971 601511.5 -601511.5
|
||||
40 215.13122 -1.1493875 -1.1493875 -1.1217969 602202.36 -602202.36
|
||||
50 187.82673 -1.1458855 -1.1458855 -1.1217966 602860.26 -602860.26
|
||||
60 164.26822 -1.1428639 -1.1428639 -1.1217965 603413.25 -603413.25
|
||||
70 146.65179 -1.1406045 -1.1406045 -1.1217964 603809.35 -603809.35
|
||||
80 136.10769 -1.1392522 -1.1392522 -1.1217964 604022.32 -604022.32
|
||||
90 132.62756 -1.138806 -1.138806 -1.1217964 604053.33 -604053.33
|
||||
100 135.19841 -1.1391358 -1.1391358 -1.1217966 603928.48 -603928.48
|
||||
Loop time of 2.19167 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 1.971 ns/day, 12.176 hours/ns, 45.627 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1547 | 2.1547 | 2.1547 | 0.0 | 98.32
|
||||
Neigh | 0.033584 | 0.033584 | 0.033584 | 0.0 | 1.53
|
||||
Comm | 0.001943 | 0.001943 | 0.001943 | 0.0 | 0.09
|
||||
Output | 0.000658 | 0.000658 | 0.000658 | 0.0 | 0.03
|
||||
Modify | 0.000365 | 0.000365 | 0.000365 | 0.0 | 0.02
|
||||
Other | | 0.000379 | | | 0.02
|
||||
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727.000 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3712.00 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424.00 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58.000000
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:02
|
||||
Reference in New Issue
Block a user