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lammps/examples/threebody/log.27Nov18.threebody.g++.4

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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 2 by 2 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 = 0.000348091 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) = 2.957 | 2.957 | 2.957 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1800 -2220.3392 0 -2101.4457 12358.626
10 979.93888 -2165.9769 0 -2101.3242 14172.134
20 579.6159 -2139.1412 0 -2101.3085 11866.038
30 1027.5223 -2167.6187 0 -2101.3942 6885.6751
40 711.03138 -2145.0665 0 -2101.3405 6357.0866
50 497.18304 -2129.9748 0 -2101.3052 7137.6093
60 1008.411 -2162.5834 0 -2101.3804 6745.1775
70 947.58674 -2156.9872 0 -2101.3508 9678.1622
80 798.43683 -2145.8382 0 -2101.3074 12728.694
90 1259.2065 -2174.5324 0 -2101.3799 12033.395
100 1100.5203 -2161.8599 0 -2101.3468 12356.137
Loop time of 0.0414283 on 4 procs for 100 steps with 512 atoms
Performance: 208.553 ns/day, 0.115 hours/ns, 2413.811 timesteps/s
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030011 | 0.032047 | 0.034036 | 0.8 | 77.36
Neigh | 0.00043392 | 0.00045151 | 0.0004642 | 0.0 | 1.09
Comm | 0.0050831 | 0.0067263 | 0.0091536 | 1.8 | 16.24
Output | 0.00018191 | 0.00018775 | 0.00020432 | 0.0 | 0.45
Modify | 0.00068116 | 0.0010136 | 0.001817 | 1.5 | 2.45
Other | | 0.001002 | | | 2.42
Nlocal: 128 ave 132 max 126 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 525 ave 527 max 521 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3507 ave 3596 max 3470 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 14028
Ave neighs/atom = 27.3984
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 2 by 2 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) = 2.717 | 2.718 | 2.718 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -621.61663 0 -561.10352 462716.2
110 1478.2708 -644.61282 0 -561.16927 464567.29
120 1989.4577 -675.5312 0 -561.25985 486476.63
130 1185.4652 -620.23829 0 -561.09359 514103.86
140 1726.9774 -654.21952 0 -561.20676 488915.22
150 1863.2061 -660.66167 0 -561.21416 466985.15
160 1119.0313 -609.68409 0 -561.08624 471511.61
170 1708.2653 -646.79823 0 -561.18829 468697.42
180 1891.8451 -656.32585 0 -561.2042 489912.65
190 1345.7703 -618.29258 0 -561.09909 512364.68
200 1865.9507 -650.72167 0 -561.19281 491531.23
Loop time of 0.117532 on 4 procs for 100 steps with 512 atoms
Performance: 73.512 ns/day, 0.326 hours/ns, 850.834 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096347 | 0.10005 | 0.10244 | 0.8 | 85.13
Neigh | 0.000947 | 0.0010053 | 0.0011535 | 0.3 | 0.86
Comm | 0.0098422 | 0.012949 | 0.016335 | 2.2 | 11.02
Output | 0.00017452 | 0.00022596 | 0.00037885 | 0.0 | 0.19
Modify | 0.00078702 | 0.0013881 | 0.0021975 | 1.6 | 1.18
Other | | 0.001909 | | | 1.62
Nlocal: 128 ave 133 max 125 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 754.5 ave 759 max 748 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4353 ave 4512 max 4252 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 17412
Ave neighs/atom = 34.0078
Neighbor list builds = 3
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 2 by 2 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) = 2.739 | 2.739 | 2.739 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -1495.2135 0 -1434.7004 357102.51
110 1238.7371 -1502.5372 0 -1434.7528 348870.19
120 1409.575 -1511.3137 0 -1434.7612 336831.6
130 1081.541 -1487.5554 0 -1434.6881 339244.71
140 1484.7455 -1512.0076 0 -1434.7646 313026.51
150 1263.0321 -1494.834 0 -1434.7018 306496.02
160 1253.4363 -1492.1804 0 -1434.7025 290683.01
170 1536.7348 -1508.3735 0 -1434.7312 261755.69
180 1342.0478 -1493.0615 0 -1434.6754 248519.54
190 1457.921 -1498.4355 0 -1434.6991 223607.39
200 1499.5384 -1498.7005 0 -1434.6898 204647.17
Loop time of 0.060006 on 4 procs for 100 steps with 512 atoms
Performance: 143.986 ns/day, 0.167 hours/ns, 1666.501 timesteps/s
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043862 | 0.047754 | 0.04964 | 1.0 | 79.58
Neigh | 0.0018079 | 0.0018883 | 0.0019724 | 0.1 | 3.15
Comm | 0.0067413 | 0.0083464 | 0.011978 | 2.3 | 13.91
Output | 0.00018859 | 0.00029892 | 0.00062919 | 0.0 | 0.50
Modify | 0.00088429 | 0.0011829 | 0.0014911 | 0.8 | 1.97
Other | | 0.0005357 | | | 0.89
Nlocal: 128 ave 129 max 127 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 992.75 ave 1001 max 987 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9116 ave 9213 max 9051 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 36464
Ave neighs/atom = 71.2188
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 2 by 2 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) = 2.699 | 2.699 | 2.699 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -3252.8699 0 -3192.3567 1930742.5
110 1858.7735 -3301.1227 0 -3192.8403 1901753.1
120 1107.7693 -3248.8236 0 -3192.2522 1953649.4
130 1315.4397 -3260.1471 0 -3192.2616 1898713.9
140 1541.4371 -3273.1832 0 -3192.41 1887352.3
150 1424.7104 -3262.9648 0 -3192.216 1960688.1
160 1291.2932 -3251.5548 0 -3192.0201 1914541.2
170 1719.1133 -3277.7936 0 -3192.33 1893926
180 1312.8066 -3248.6914 0 -3192.1477 1921417.4
190 1481.3472 -3257.1585 0 -3191.8991 1927045.6
200 1615.282 -3263.8377 0 -3192.055 1920616.3
Loop time of 0.0635643 on 4 procs for 100 steps with 512 atoms
Performance: 135.925 ns/day, 0.177 hours/ns, 1573.210 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.051391 | 0.053262 | 0.05459 | 0.6 | 83.79
Neigh | 0.00052404 | 0.00052798 | 0.00053144 | 0.0 | 0.83
Comm | 0.0063059 | 0.0079132 | 0.0095143 | 1.5 | 12.45
Output | 0.00017905 | 0.00029147 | 0.00062609 | 0.0 | 0.46
Modify | 0.00064421 | 0.00096625 | 0.0012674 | 0.0 | 1.52
Other | | 0.0006039 | | | 0.95
Nlocal: 128 ave 131 max 125 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 526.75 ave 532 max 523 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3646.5 ave 3722 max 3567 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 14586
Ave neighs/atom = 28.4883
Neighbor list builds = 2
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 2 by 2 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) = 2.701 | 2.701 | 2.701 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -2308.936 0 -2248.4229 18087.231
110 821.82813 -2288.8477 0 -2248.3856 21245.995
120 1082.3774 -2304.2287 0 -2248.4366 15467.483
130 995.26561 -2296.2957 0 -2248.4145 16341.517
140 826.97009 -2283.3692 0 -2248.3897 19123.5
150 1048.4178 -2296.0496 0 -2248.4172 15060.312
160 1101.7884 -2297.2417 0 -2248.426 15070.879
170 859.48562 -2279.1747 0 -2248.383 21416.479
180 1041.679 -2289.2303 0 -2248.4038 19572.707
190 1278.0514 -2302.2822 0 -2248.4257 16006.173
200 1097.0682 -2287.8121 0 -2248.3929 20906.774
Loop time of 0.046846 on 4 procs for 100 steps with 512 atoms
Performance: 184.434 ns/day, 0.130 hours/ns, 2134.653 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037434 | 0.039142 | 0.041109 | 0.7 | 83.55
Neigh | 0.0005877 | 0.00059921 | 0.00061464 | 0.0 | 1.28
Comm | 0.0036416 | 0.0055436 | 0.0073476 | 1.8 | 11.83
Output | 0.00016212 | 0.00027066 | 0.00059533 | 0.0 | 0.58
Modify | 0.00063038 | 0.00065678 | 0.00067234 | 0.0 | 1.40
Other | | 0.0006335 | | | 1.35
Nlocal: 128 ave 131 max 126 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 518 ave 525 max 513 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2202 ave 2257 max 2175 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 8808
Ave neighs/atom = 17.2031
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 2 by 2 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) = 2.701 | 2.701 | 2.701 Mbytes
Step Temp E_pair E_mol TotEng Press
100 1100.5203 -2308.5955 0 -2248.0824 20775.991
110 813.33618 -2287.9469 0 -2248.04 22564.16
120 1100.0902 -2305.051 0 -2248.092 17540.971
130 1022.9471 -2297.7384 0 -2248.0801 17985.336
140 761.99242 -2278.7251 0 -2248.0345 20462.975
150 1053.3973 -2296.1039 0 -2248.081 16130.559
160 1089.2622 -2296.1059 0 -2248.0833 15434.234
170 776.25788 -2273.4496 0 -2248.0321 20642.702
180 1016.1885 -2287.4305 0 -2248.0641 19276.936
190 1266.3943 -2301.3675 0 -2248.0865 16199.281
200 1012.4185 -2282.134 0 -2248.0423 20795.113
Loop time of 0.0840016 on 4 procs for 100 steps with 512 atoms
Performance: 102.855 ns/day, 0.233 hours/ns, 1190.454 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068133 | 0.071658 | 0.075315 | 1.0 | 85.31
Neigh | 0.00057864 | 0.00058872 | 0.00060058 | 0.0 | 0.70
Comm | 0.0049844 | 0.008617 | 0.012086 | 2.8 | 10.26
Output | 0.0001626 | 0.00027418 | 0.00060463 | 0.0 | 0.33
Modify | 0.00070477 | 0.0011689 | 0.0022428 | 1.8 | 1.39
Other | | 0.001694 | | | 2.02
Nlocal: 128 ave 129 max 127 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 489.75 ave 501 max 481 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 2094.5 ave 2121 max 2060 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 8378
Ave neighs/atom = 16.3633
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00
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