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lammps/examples/threebody/log.08Feb21.threebody.g++.4

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LAMMPS (24 Dec 2020)
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 = 5.4310000 5.4310000 5.4310000
region myreg block 0 4 0 4 0 4
create_box 8 myreg
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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
create_atoms CPU = 0.074 seconds
mass * 28.06
velocity all create $t 5287287 loop geom
velocity all create 1800 5287287 loop geom
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
Reading sw potential file Si.sw with DATE: 2007-06-11
thermo_style custom step temp epair etotal econserve press
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
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) = 2.958 | 2.958 | 2.958 Mbytes
Step Temp E_pair TotEng Econserve Press
0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
Loop time of 0.0998364 on 4 procs for 100 steps with 512 atoms
Performance: 86.542 ns/day, 0.277 hours/ns, 1001.639 timesteps/s
81.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037337 | 0.049389 | 0.069239 | 5.9 | 49.47
Neigh | 0.00067854 | 0.00068814 | 0.00070286 | 0.0 | 0.69
Comm | 0.025239 | 0.04504 | 0.056869 | 6.1 | 45.11
Output | 0.00015712 | 0.00082219 | 0.0028148 | 0.0 | 0.82
Modify | 0.0014369 | 0.0015754 | 0.0016632 | 0.2 | 1.58
Other | | 0.002321 | | | 2.33
Nlocal: 128.000 ave 132 max 125 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 525.000 ave 528 max 521 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3497.00 ave 3619 max 3397 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 13988
Ave neighs/atom = 27.320312
Neighbor list builds = 2
Dangerous builds = 0
write_restart restart.equil
System init for write_restart ...
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
using 1 OpenMP thread(s) per MPI task
read_restart restart.equil
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
thermo_style custom step temp epair etotal econserve press
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
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 = 5.6320004
ghost atom cutoff = 5.6320004
binsize = 2.8160002, 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) = 2.967 | 2.967 | 2.968 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -625.76163 -552.24782 -564.38354 462129.66
110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
120 1926.4523 -674.71265 -547.46675 -564.53613 486338.88
130 1152.6663 -621.47265 -545.33681 -564.37203 514892.19
140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
150 1767.8665 -657.67179 -540.90079 -564.48386 466721.31
160 1075.2874 -610.1281 -539.10328 -564.36709 470151.9
170 1697.9313 -649.3684 -537.21676 -564.47208 467953.7
180 1856.1197 -657.14338 -534.54309 -564.48754 488372.26
190 1346.1107 -621.42432 -532.5111 -564.38065 511750.03
200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
Loop time of 0.286556 on 4 procs for 100 steps with 512 atoms
Performance: 30.151 ns/day, 0.796 hours/ns, 348.971 timesteps/s
81.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11093 | 0.139 | 0.16864 | 5.8 | 48.51
Neigh | 0.0014305 | 0.0014756 | 0.0015156 | 0.1 | 0.51
Comm | 0.10154 | 0.12374 | 0.16907 | 7.8 | 43.18
Output | 0.0001862 | 0.00030428 | 0.0006578 | 0.0 | 0.11
Modify | 0.0038164 | 0.019159 | 0.034146 | 10.8 | 6.69
Other | | 0.002872 | | | 1.00
Nlocal: 128.000 ave 135 max 122 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 759.750 ave 770 max 751 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4336.00 ave 4563 max 4128 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 17344
Ave neighs/atom = 33.875000
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
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.001 seconds
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
thermo_style custom step temp epair etotal econserve press
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
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) = 2.988 | 2.988 | 2.988 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
Loop time of 0.14468 on 4 procs for 100 steps with 512 atoms
Performance: 59.718 ns/day, 0.402 hours/ns, 691.179 timesteps/s
81.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.047903 | 0.058669 | 0.086091 | 6.6 | 40.55
Neigh | 0.0027876 | 0.002852 | 0.0028808 | 0.1 | 1.97
Comm | 0.034642 | 0.066142 | 0.078599 | 7.1 | 45.72
Output | 0.00018477 | 0.0049147 | 0.019101 | 11.7 | 3.40
Modify | 0.0015709 | 0.0022651 | 0.0029545 | 1.4 | 1.57
Other | | 0.009837 | | | 6.80
Nlocal: 128.000 ave 131 max 124 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 1013.25 ave 1025 max 1002 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 9120.50 ave 9356 max 8868 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 36482
Ave neighs/atom = 71.253906
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
Reading restart file ...
restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020
restoring atom style atomic from restart
orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
1 by 2 by 2 MPI processor grid
pair style sw stores no restart info
512 atoms
read_restart CPU = 0.005 seconds
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
Changing box ...
orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
thermo_style custom step temp epair etotal econserve press
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
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) = 2.948 | 2.948 | 2.948 Mbytes
Step Temp E_pair TotEng Econserve Press
100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
Loop time of 0.348631 on 4 procs for 100 steps with 512 atoms
Performance: 24.783 ns/day, 0.968 hours/ns, 286.836 timesteps/s
81.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13281 | 0.15657 | 0.20106 | 6.9 | 44.91
Neigh | 0.00037527 | 0.00039309 | 0.00040412 | 0.0 | 0.11
Comm | 0.12177 | 0.16672 | 0.19154 | 6.8 | 47.82
Output | 0.00019097 | 0.000462 | 0.0012722 | 0.0 | 0.13
Modify | 0.018353 | 0.020198 | 0.02302 | 1.3 | 5.79
Other | | 0.004286 | | | 1.23
Nlocal: 128.000 ave 132 max 123 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 529.500 ave 533 max 524 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 3651.00 ave 3783 max 3494 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 14604
Ave neighs/atom = 28.523438
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01
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