470 lines
20 KiB
Groff
470 lines
20 KiB
Groff
LAMMPS (29 Sep 2021 - Update 3)
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using 1 OpenMP thread(s) per MPI task
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# Simple regression tests for threebody potentials
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# NOTE: These are not intended to represent real materials
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# cubic diamond unit cell
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variable a equal 5.431
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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
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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
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Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
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region myreg block 0 4 0 4 0 4
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create_box 8 myreg
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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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
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Created 512 atoms
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using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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create_atoms CPU = 0.000 seconds
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mass * 28.06
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velocity all create $t 5287287 loop geom
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velocity all create 1800 5287287 loop geom
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# Equilibrate using Stillinger-Weber model for silicon
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pair_style sw
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pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
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Reading sw potential file Si.sw with DATE: 2007-06-11
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thermo_style custom step temp epair etotal econserve press
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 4.77118
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ghost atom cutoff = 4.77118
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binsize = 2.38559, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sw, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 Mbytes
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Step Temp E_pair TotEng Econserve Press
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0 1800 -2220.3392 -2101.4457 -2101.4457 12358.626
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10 1006.0192 -2167.7053 -2101.2558 -2101.3286 13892.426
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20 588.26396 -2139.7132 -2100.8573 -2101.3117 11295.566
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30 990.55956 -2165.2164 -2099.788 -2101.3931 6279.0239
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40 700.12917 -2144.4279 -2098.183 -2101.3427 5594.2388
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50 523.64239 -2131.7796 -2097.192 -2101.3122 6013.0994
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60 989.47092 -2161.3716 -2096.0152 -2101.3839 5819.2688
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70 877.27433 -2152.4432 -2094.4975 -2101.3461 9116.6569
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80 800.80221 -2146.1371 -2093.2426 -2101.313 11995.66
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90 1293.9689 -2176.9021 -2091.4329 -2101.3848 11692.45
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100 1112.9699 -2162.7259 -2089.2121 -2101.3478 12263.758
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Loop time of 0.093281 on 1 procs for 100 steps with 512 atoms
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Performance: 92.623 ns/day, 0.259 hours/ns, 1072.029 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.090256 | 0.090256 | 0.090256 | 0.0 | 96.76
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Neigh | 0.0015078 | 0.0015078 | 0.0015078 | 0.0 | 1.62
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Comm | 0.00045896 | 0.00045896 | 0.00045896 | 0.0 | 0.49
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Output | 8.3447e-05 | 8.3447e-05 | 8.3447e-05 | 0.0 | 0.09
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Modify | 0.00072384 | 0.00072384 | 0.00072384 | 0.0 | 0.78
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Other | | 0.0002506 | | | 0.27
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1017.00 ave 1017 max 1017 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 13988.0 ave 13988 max 13988 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 13988
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Ave neighs/atom = 27.320312
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Neighbor list builds = 2
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Dangerous builds = 0
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write_restart restart.equil
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System init for write_restart ...
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# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style sw stores no restart info
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512 atoms
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read_restart CPU = 0.000 seconds
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pair_style sw
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pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
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Reading sw potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09
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thermo_style custom step temp epair etotal econserve press
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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All restart file global fix info was re-assigned
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.6320004
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ghost atom cutoff = 5.6320004
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binsize = 2.8160002, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sw, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes
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Step Temp E_pair TotEng Econserve Press
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100 1112.9699 -625.76163 -552.24781 -564.38354 462129.66
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110 1502.8461 -649.55768 -550.29179 -564.45814 463413.45
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120 1926.4523 -674.71265 -547.46675 -564.53612 486338.88
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130 1152.6663 -621.47264 -545.33681 -564.37203 514892.2
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140 1762.244 -659.86941 -543.46979 -564.4985 488159.88
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150 1767.8665 -657.67178 -540.90078 -564.48386 466721.31
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160 1075.2874 -610.12809 -539.10328 -564.36709 470151.9
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170 1697.9313 -649.3684 -537.21675 -564.47207 467953.71
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180 1856.1197 -657.14338 -534.54309 -564.48754 488372.27
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190 1346.1107 -621.42431 -532.5111 -564.38065 511750.04
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200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56
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Loop time of 0.245572 on 1 procs for 100 steps with 512 atoms
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Performance: 35.183 ns/day, 0.682 hours/ns, 407.212 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.24139 | 0.24139 | 0.24139 | 0.0 | 98.30
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Neigh | 0.0027068 | 0.0027068 | 0.0027068 | 0.0 | 1.10
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Comm | 0.00051188 | 0.00051188 | 0.00051188 | 0.0 | 0.21
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Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.04
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Modify | 0.00059605 | 0.00059605 | 0.00059605 | 0.0 | 0.24
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Other | | 0.0002608 | | | 0.11
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1428.00 ave 1428 max 1428 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 17344.0 ave 17344 max 17344 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 17344
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Ave neighs/atom = 33.875000
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Neighbor list builds = 3
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Dangerous builds = 0
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# Test Vashishta model for In/P
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style sw stores no restart info
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512 atoms
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read_restart CPU = 0.000 seconds
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pair_style vashishta
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pair_coeff * * InP.vashishta In In In In P P P P
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Reading vashishta potential file InP.vashishta with DATE: 2015-10-14
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thermo_style custom step temp epair etotal econserve press
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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All restart file global fix info was re-assigned
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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binsize = 3.5, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair vashishta, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
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Step Temp E_pair TotEng Econserve Press
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100 1112.9699 -1497.2988 -1423.785 -1435.9207 355619.19
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110 1250.545 -1504.5795 -1421.9785 -1435.9786 345188.52
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120 1360.2275 -1509.3443 -1419.4986 -1435.9801 333306.3
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130 1066.4516 -1487.9076 -1417.4664 -1435.9076 334465.11
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140 1481.0477 -1513.0511 -1415.2251 -1435.988 308725.1
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150 1216.1167 -1493.0774 -1412.7505 -1435.9217 304249.09
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160 1211.4398 -1490.7459 -1410.728 -1435.9164 288897.09
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170 1542.2025 -1510.0774 -1408.212 -1435.9608 260104.14
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180 1302.9041 -1491.7765 -1405.7172 -1435.8971 249514.04
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190 1332.3326 -1491.5271 -1403.524 -1435.9213 227537.99
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200 1352.1813 -1490.4513 -1401.1371 -1435.9049 207626.42
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Loop time of 0.111899 on 1 procs for 100 steps with 512 atoms
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Performance: 77.212 ns/day, 0.311 hours/ns, 893.662 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.10539 | 0.10539 | 0.10539 | 0.0 | 94.18
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Neigh | 0.0049229 | 0.0049229 | 0.0049229 | 0.0 | 4.40
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Comm | 0.00068307 | 0.00068307 | 0.00068307 | 0.0 | 0.61
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Output | 6.1989e-05 | 6.1989e-05 | 6.1989e-05 | 0.0 | 0.06
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Modify | 0.00058532 | 0.00058532 | 0.00058532 | 0.0 | 0.52
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Other | | 0.0002604 | | | 0.23
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1838.00 ave 1838 max 1838 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 36482.0 ave 36482 max 36482 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 36482
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Ave neighs/atom = 71.253906
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Neighbor list builds = 4
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Dangerous builds = 0
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# Test Tersoff model for B/N/C
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style sw stores no restart info
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512 atoms
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read_restart CPU = 0.000 seconds
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variable fac equal 0.6
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change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
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change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
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change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
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change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
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Changing box ...
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orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
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orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
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orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
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pair_style tersoff
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pair_coeff * * BNC.tersoff N N N C B B C B
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Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
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thermo_style custom step temp epair etotal econserve press
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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run 100
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All restart file global fix info was re-assigned
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.1
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ghost atom cutoff = 3.1
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binsize = 1.55, bins = 9 9 9
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tersoff, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes
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Step Temp E_pair TotEng Econserve Press
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100 1112.9699 -3259.7676 -3186.2538 -3198.3895 1912461.3
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110 1772.8268 -3301.5479 -3184.4493 -3198.8218 1885295.6
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120 1169.7287 -3258.74 -3181.4772 -3197.9294 1898705.2
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130 1308.5623 -3265.1338 -3178.7007 -3197.5922 1894187.5
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140 1486.0361 -3274.951 -3176.7954 -3197.776 1871927.6
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150 1419.0362 -3267.7302 -3174.0002 -3197.2296 1925234.6
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160 1196.6689 -3250.1492 -3171.1069 -3196.7078 1902235.1
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170 1707.5846 -3281.7658 -3168.9766 -3196.9721 1863047.3
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180 1337.4358 -3254.9844 -3166.6442 -3196.8222 1880420.9
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190 1441.8052 -3259.0364 -3163.8023 -3196.3556 1904512.1
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200 1569.0317 -3265.0089 -3161.3714 -3196.3328 1899462.7
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Loop time of 0.097734 on 1 procs for 100 steps with 512 atoms
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Performance: 88.403 ns/day, 0.271 hours/ns, 1023.186 timesteps/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.095481 | 0.095481 | 0.095481 | 0.0 | 97.69
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Neigh | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.79
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Comm | 0.00046158 | 0.00046158 | 0.00046158 | 0.0 | 0.47
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Output | 6.7949e-05 | 6.7949e-05 | 6.7949e-05 | 0.0 | 0.07
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Modify | 0.00068784 | 0.00068784 | 0.00068784 | 0.0 | 0.70
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Other | | 0.0002635 | | | 0.27
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Nlocal: 512.000 ave 512 max 512 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1028.00 ave 1028 max 1028 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 14604.0 ave 14604 max 14604 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 14604
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Ave neighs/atom = 28.523438
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Neighbor list builds = 1
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Dangerous builds = 0
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# Test Tersoff/ZBL model for SiC
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart restart.equil
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Reading restart file ...
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restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021
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restoring atom style atomic from restart
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000)
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1 by 1 by 1 MPI processor grid
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pair style sw stores no restart info
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512 atoms
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read_restart CPU = 0.000 seconds
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variable fac equal 0.6
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change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
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change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap
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change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap
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change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap
|
|
Changing box ...
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orthogonal box = (4.3448000 0.0000000 0.0000000) to (17.379200 21.724000 21.724000)
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orthogonal box = (4.3448000 4.3448000 0.0000000) to (17.379200 17.379200 21.724000)
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orthogonal box = (4.3448000 4.3448000 4.3448000) to (17.379200 17.379200 17.379200)
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|
|
pair_style tersoff/zbl
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|
pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si
|
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Reading tersoff/zbl potential file SiC.tersoff.zbl with DATE: 2009-04-15
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|
|
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thermo_style custom step temp epair etotal econserve press
|
|
thermo 10
|
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fix 1 all nvt temp $t $t 0.1
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|
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:
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|
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 = 4
|
|
ghost atom cutoff = 4
|
|
binsize = 2, bins = 7 7 7
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair tersoff/zbl, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.002 | 3.002 | 3.002 Mbytes
|
|
Step Temp E_pair TotEng Econserve Press
|
|
100 1112.9699 7067.9634 7141.4772 7129.3415 17683957
|
|
110 1676.669 7033.1458 7143.893 7128.6921 17837566
|
|
120 2450.2667 6982.2491 7144.094 7126.9524 18220027
|
|
130 2726.9659 6964.1219 7144.2432 7126.7678 18230324
|
|
140 2729.421 6962.7393 7143.0228 7127.2074 18176317
|
|
150 2738.5449 6959.1761 7140.0623 7127.6671 18068370
|
|
160 2687.2419 6958.1183 7135.6158 7127.8492 18156214
|
|
170 2697.7325 6952.1482 7130.3387 7127.7898 17978251
|
|
180 2577.9885 6954.5611 7124.8422 7127.5615 18068920
|
|
190 2502.6928 6954.4558 7119.7635 7127.67 18049652
|
|
200 2517.4866 6947.962 7114.2469 7127.1972 18209451
|
|
Loop time of 0.783169 on 1 procs for 100 steps with 512 atoms
|
|
|
|
Performance: 11.032 ns/day, 2.175 hours/ns, 127.686 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 | 0.78056 | 0.78056 | 0.78056 | 0.0 | 99.67
|
|
Neigh | 0.0011299 | 0.0011299 | 0.0011299 | 0.0 | 0.14
|
|
Comm | 0.00051332 | 0.00051332 | 0.00051332 | 0.0 | 0.07
|
|
Output | 9.2268e-05 | 9.2268e-05 | 9.2268e-05 | 0.0 | 0.01
|
|
Modify | 0.00060058 | 0.00060058 | 0.00060058 | 0.0 | 0.08
|
|
Other | | 0.0002706 | | | 0.03
|
|
|
|
Nlocal: 512.000 ave 512 max 512 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1542.00 ave 1542 max 1542 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 30142.0 ave 30142 max 30142 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 30142
|
|
Ave neighs/atom = 58.871094
|
|
Neighbor list builds = 1
|
|
Dangerous builds = 0
|
|
|
|
shell rm restart.equil
|
|
Total wall time: 0:00:01
|