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lammps/examples/threebody/log.27Nov18.threebody.g++.1

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8
Created 512 atoms
Time spent = 0.000483751 secs
mass * 28.06
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading potential file Si.sw with DATE: 2007-06-11
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 993.48824 -2166.8749 0 -2101.3265 14121.853
20 587.90768 -2139.6876 0 -2101.3093 11864.886
30 1030.8616 -2167.8446 0 -2101.3947 6649.2566
40 724.62874 -2145.9637 0 -2101.3436 5859.6447
50 490.9053 -2129.5491 0 -2101.3077 6326.5434
60 960.24533 -2159.427 0 -2101.3794 5733.9889
70 906.76518 -2154.3675 0 -2101.3496 8380.4834
80 800.7253 -2146.0714 0 -2101.3113 11515.737
90 1249.2719 -2173.9445 0 -2101.3818 11593.728
100 1080.3797 -2160.6174 0 -2101.3445 12414.602
Loop time of 0.129171 on 1 procs for 100 steps with 512 atoms
Performance: 66.888 ns/day, 0.359 hours/ns, 774.165 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12468 | 0.12468 | 0.12468 | 0.0 | 96.52
Neigh | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 1.33
Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.69
Output | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.09
Modify | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 1.11
Other | | 0.0003417 | | | 0.26
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14044 ave 14044 max 14044 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14044
Ave neighs/atom = 27.4297
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.632
ghost atom cutoff = 5.632
binsize = 2.816, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.758 | 2.758 | 2.758 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -621.93681 0 -562.66385 464005.01
110 1512.4547 -648.51133 0 -562.74194 463733.24
120 1959.7565 -675.18668 0 -562.8255 486580.33
130 1138.5498 -618.80419 0 -562.6427 515406.41
140 1827.3403 -662.43867 0 -562.78985 485719
150 1822.9803 -659.56725 0 -562.76627 465652.59
160 1128.3444 -611.92808 0 -562.65512 469836.33
170 1699.6402 -647.82381 0 -562.75353 467977.54
180 1840.047 -654.5552 0 -562.77005 488397.41
190 1312.0974 -617.70228 0 -562.6629 510856.48
200 1809.8409 -648.6173 0 -562.75377 490822.97
Loop time of 0.399255 on 1 procs for 100 steps with 512 atoms
Performance: 21.640 ns/day, 1.109 hours/ns, 250.467 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38979 | 0.38979 | 0.38979 | 0.0 | 97.63
Neigh | 0.0061283 | 0.0061283 | 0.0061283 | 0.0 | 1.53
Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.34
Output | 0.00016642 | 0.00016642 | 0.00016642 | 0.0 | 0.04
Modify | 0.0014937 | 0.0014937 | 0.0014937 | 0.0 | 0.37
Other | | 0.0003231 | | | 0.08
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1386 ave 1386 max 1386 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17388 ave 17388 max 17388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 17388
Ave neighs/atom = 33.9609
Neighbor list builds = 5
Dangerous builds = 0
# Test Vashishta model for In/P
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading potential file InP.vashishta with DATE: 2015-10-14
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair vashishta, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.783 | 2.783 | 2.783 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -1491.8652 0 -1432.5922 358930.65
110 1299.3069 -1504.494 0 -1432.6803 347566.41
120 1396.3035 -1508.3817 0 -1432.672 336798.42
130 1055.9254 -1483.8342 0 -1432.5849 341035.18
140 1543.9033 -1513.8559 0 -1432.6931 314268.54
150 1242.5383 -1491.417 0 -1432.6036 311068.53
160 1240.1733 -1489.2495 0 -1432.6033 295776.98
170 1559.5037 -1507.824 0 -1432.6417 266170.25
180 1379.0358 -1493.4092 0 -1432.5869 251410.63
190 1465.8073 -1496.8564 0 -1432.6105 226461.31
200 1456.6383 -1493.8133 0 -1432.5852 208188.34
Loop time of 0.198058 on 1 procs for 100 steps with 512 atoms
Performance: 43.624 ns/day, 0.550 hours/ns, 504.903 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.18746 | 0.18746 | 0.18746 | 0.0 | 94.65
Neigh | 0.00688 | 0.00688 | 0.00688 | 0.0 | 3.47
Comm | 0.001718 | 0.001718 | 0.001718 | 0.0 | 0.87
Output | 0.00013351 | 0.00013351 | 0.00013351 | 0.0 | 0.07
Modify | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.76
Other | | 0.0003531 | | | 0.18
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1810 ave 1810 max 1810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 36480 ave 36480 max 36480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36480
Ave neighs/atom = 71.25
Neighbor list builds = 4
Dangerous builds = 0
# Test Tersoff model for B/N/C
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724)
orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724)
orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading potential file BNC.tersoff with DATE: 2013-03-21
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.1
ghost atom cutoff = 3.1
binsize = 1.55, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.74 | 2.74 | 2.74 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -3249.8451 0 -3190.5722 1925371.8
110 1878.2843 -3300.7205 0 -3191.0964 1893058.6
120 1153.8494 -3250.2114 0 -3190.5436 1932141.4
130 1363.8664 -3261.6889 0 -3190.6116 1902268.1
140 1565.5505 -3273.0405 0 -3190.6982 1878817
150 1416.9458 -3261.1805 0 -3190.865 1916554.4
160 1288.6997 -3249.8279 0 -3190.4141 1933227.4
170 1768.3043 -3279.2164 0 -3190.4535 1898123.4
180 1375.1942 -3251.0929 0 -3190.3781 1896205.1
190 1527.0671 -3258.7679 0 -3190.4344 1900673.6
200 1586.8691 -3260.4713 0 -3190.434 1912454.8
Loop time of 0.210082 on 1 procs for 100 steps with 512 atoms
Performance: 41.127 ns/day, 0.584 hours/ns, 476.006 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20628 | 0.20628 | 0.20628 | 0.0 | 98.19
Neigh | 0.00099182 | 0.00099182 | 0.00099182 | 0.0 | 0.47
Comm | 0.00085139 | 0.00085139 | 0.00085139 | 0.0 | 0.41
Output | 0.00013494 | 0.00013494 | 0.00013494 | 0.0 | 0.06
Modify | 0.0014665 | 0.0014665 | 0.0014665 | 0.0 | 0.70
Other | | 0.0003612 | | | 0.17
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1027 ave 1027 max 1027 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 14602 ave 14602 max 14602 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14602
Ave neighs/atom = 28.5195
Neighbor list builds = 1
Dangerous builds = 0
# Test Tersoff/Mod model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
pair_style tersoff/mod
pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.mod with DATE: 2013-07-26
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.744 | 2.744 | 2.744 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -2307.5808 0 -2248.3078 18624.75
110 851.21757 -2290.7529 0 -2248.2817 21041.97
120 1074.6349 -2303.6437 0 -2248.321 15244.809
130 1006.5662 -2296.9866 0 -2248.3057 15954.09
140 855.64354 -2285.1581 0 -2248.2781 19346.662
150 1111.1546 -2300.024 0 -2248.314 14698.998
160 1114.7933 -2297.8629 0 -2248.3098 14414.14
170 853.9568 -2278.6047 0 -2248.2716 20120.632
180 1031.0925 -2288.3481 0 -2248.2949 18332.008
190 1230.3458 -2298.9946 0 -2248.3111 15520.302
200 1053.8799 -2284.8931 0 -2248.2816 20033.536
Loop time of 0.158428 on 1 procs for 100 steps with 512 atoms
Performance: 54.536 ns/day, 0.440 hours/ns, 631.200 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15318 | 0.15318 | 0.15318 | 0.0 | 96.69
Neigh | 0.0022631 | 0.0022631 | 0.0022631 | 0.0 | 1.43
Comm | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.59
Output | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.12
Modify | 0.0015035 | 0.0015035 | 0.0015035 | 0.0 | 0.95
Other | | 0.0003462 | | | 0.22
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1001 ave 1001 max 1001 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 8872 ave 8872 max 8872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8872
Ave neighs/atom = 17.3281
Neighbor list builds = 3
Dangerous builds = 0
# Test Tersoff/Mod/C model for Si
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
pair style sw stores no restart info
512 atoms
newton on on
pair_style tersoff/mod/c
pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si
Reading potential file Si.tersoff.modc with DATE: 2016-11-09
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.20569
ghost atom cutoff = 4.20569
binsize = 2.10285, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/mod/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1080.3797 -2307.5509 0 -2248.2779 21368.36
110 846.70637 -2290.4239 0 -2248.2488 22856.37
120 1083.0906 -2304.1686 0 -2248.2895 17530.457
130 1008.7015 -2297.0835 0 -2248.2781 17698.498
140 811.71413 -2282.2528 0 -2248.2417 19986.737
150 1094.4969 -2298.9718 0 -2248.2836 15822.967
160 1100.1109 -2296.9461 0 -2248.2804 15213.75
170 801.20165 -2275.2175 0 -2248.2372 20153.957
180 994.63485 -2286.1145 0 -2248.2621 19167.021
190 1215.6425 -2298.2082 0 -2248.284 15895.654
200 992.20385 -2281.0372 0 -2248.2425 19643.792
Loop time of 0.282035 on 1 procs for 100 steps with 512 atoms
Performance: 30.634 ns/day, 0.783 hours/ns, 354.565 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27701 | 0.27701 | 0.27701 | 0.0 | 98.22
Neigh | 0.0021927 | 0.0021927 | 0.0021927 | 0.0 | 0.78
Comm | 0.00089169 | 0.00089169 | 0.00089169 | 0.0 | 0.32
Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.05
Modify | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.52
Other | | 0.0003295 | | | 0.12
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 972 ave 972 max 972 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 8390 ave 8390 max 8390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 8390
Ave neighs/atom = 16.3867
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:01
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