diff --git a/examples/threebody/SiC.tersoff.zbl b/examples/threebody/SiC.tersoff.zbl new file mode 120000 index 0000000000..300116f5a6 --- /dev/null +++ b/examples/threebody/SiC.tersoff.zbl @@ -0,0 +1 @@ +../../potentials/SiC.tersoff.zbl \ No newline at end of file diff --git a/examples/threebody/in.threebody b/examples/threebody/in.threebody index 3d11219a47..e190dac8b5 100644 --- a/examples/threebody/in.threebody +++ b/examples/threebody/in.threebody @@ -7,7 +7,7 @@ units metal atom_style atomic atom_modify map array boundary p p p -atom_modify sort 0 0.0 +atom_modify sort 0 0.0 # temperature @@ -35,23 +35,23 @@ region myreg block 0 4 & create_box 8 myreg 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 + basis 1 1 & + basis 2 2 & + basis 3 3 & + basis 4 4 & + basis 5 5 & + basis 6 6 & + basis 7 7 & + basis 8 8 mass * 28.06 -velocity all create $t 5287287 loop geom +velocity all create $t 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 +pair_coeff * * Si.sw Si Si Si Si Si Si Si Si thermo_style custom step temp epair etotal econserve press thermo 10 @@ -61,15 +61,15 @@ neighbor 1.0 bin neigh_modify every 1 delay 10 check yes run 100 -write_restart restart.equil +write_restart restart.equil # Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S clear -read_restart restart.equil +read_restart restart.equil pair_style sw -pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te +pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te thermo_style custom step temp epair etotal econserve press thermo 10 @@ -82,10 +82,10 @@ run 100 # Test Vashishta model for In/P clear -read_restart restart.equil +read_restart restart.equil pair_style vashishta -pair_coeff * * InP.vashishta In In In In P P P P +pair_coeff * * InP.vashishta In In In In P P P P thermo_style custom step temp epair etotal econserve press thermo 10 @@ -98,13 +98,13 @@ run 100 # Test Tersoff model for B/N/C clear -read_restart restart.equil +read_restart restart.equil -variable fac equal 0.6 -change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap +variable fac equal 0.6 +change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap pair_style tersoff -pair_coeff * * BNC.tersoff N N N C B B C B +pair_coeff * * BNC.tersoff N N N C B B C B thermo_style custom step temp epair etotal econserve press thermo 10 @@ -114,3 +114,23 @@ neighbor 1.0 bin neigh_modify every 1 delay 10 check yes run 100 +# Test Tersoff/ZBL model for SiC + +clear +read_restart restart.equil + +variable fac equal 0.6 +change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap + +pair_style tersoff/zbl +pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si + +thermo_style custom step temp epair etotal econserve press +thermo 10 +fix 1 all nvt temp $t $t 0.1 +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 + +shell rm restart.equil diff --git a/examples/threebody/log.08Feb21.threebody.g++.1 b/examples/threebody/log.29Sep21.threebody.g++.1 similarity index 62% rename from examples/threebody/log.08Feb21.threebody.g++.1 rename to examples/threebody/log.29Sep21.threebody.g++.1 index 51b6dfea05..5bdafb78d1 100644 --- a/examples/threebody/log.08Feb21.threebody.g++.1 +++ b/examples/threebody/log.29Sep21.threebody.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (24 Dec 2020) +LAMMPS (29 Sep 2021 - Update 3) using 1 OpenMP thread(s) per MPI task # Simple regression tests for threebody potentials @@ -9,7 +9,7 @@ units metal atom_style atomic atom_modify map array boundary p p p -atom_modify sort 0 0.0 +atom_modify sort 0 0.0 # temperature @@ -27,19 +27,20 @@ region myreg block 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 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 +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 = 0.001 seconds + using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) + create_atoms CPU = 0.000 seconds mass * 28.06 -velocity all create $t 5287287 loop geom -velocity all create 1800 5287287 loop geom +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 +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 @@ -76,20 +77,20 @@ Step Temp E_pair TotEng Econserve Press 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 0.157871 on 1 procs for 100 steps with 512 atoms +Loop time of 0.093281 on 1 procs for 100 steps with 512 atoms -Performance: 54.728 ns/day, 0.439 hours/ns, 633.430 timesteps/s +Performance: 92.623 ns/day, 0.259 hours/ns, 1072.029 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14704 | 0.14704 | 0.14704 | 0.0 | 93.14 -Neigh | 0.00247 | 0.00247 | 0.00247 | 0.0 | 1.56 -Comm | 0.0024729 | 0.0024729 | 0.0024729 | 0.0 | 1.57 -Output | 0.0002656 | 0.0002656 | 0.0002656 | 0.0 | 0.17 -Modify | 0.0050237 | 0.0050237 | 0.0050237 | 0.0 | 3.18 -Other | | 0.0006011 | | | 0.38 +Pair | 0.090256 | 0.090256 | 0.090256 | 0.0 | 96.76 +Neigh | 0.0015078 | 0.0015078 | 0.0015078 | 0.0 | 1.62 +Comm | 0.00045896 | 0.00045896 | 0.00045896 | 0.0 | 0.49 +Output | 8.3447e-05 | 8.3447e-05 | 8.3447e-05 | 0.0 | 0.09 +Modify | 0.00072384 | 0.00072384 | 0.00072384 | 0.0 | 0.78 +Other | | 0.0002506 | | | 0.27 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -105,25 +106,25 @@ Ave neighs/atom = 27.320312 Neighbor list builds = 2 Dangerous builds = 0 -write_restart restart.equil +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 +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 restoring atom style atomic from restart orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 seconds pair_style sw -pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te +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 @@ -163,20 +164,20 @@ Step Temp E_pair TotEng Econserve Press 180 1856.1197 -657.14338 -534.54309 -564.48754 488372.27 190 1346.1107 -621.42431 -532.5111 -564.38065 511750.04 200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56 -Loop time of 0.455825 on 1 procs for 100 steps with 512 atoms +Loop time of 0.245572 on 1 procs for 100 steps with 512 atoms -Performance: 18.955 ns/day, 1.266 hours/ns, 219.382 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 35.183 ns/day, 0.682 hours/ns, 407.212 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.44091 | 0.44091 | 0.44091 | 0.0 | 96.73 -Neigh | 0.0054555 | 0.0054555 | 0.0054555 | 0.0 | 1.20 -Comm | 0.0035784 | 0.0035784 | 0.0035784 | 0.0 | 0.79 -Output | 0.00024486 | 0.00024486 | 0.00024486 | 0.0 | 0.05 -Modify | 0.0050471 | 0.0050471 | 0.0050471 | 0.0 | 1.11 -Other | | 0.000592 | | | 0.13 +Pair | 0.24139 | 0.24139 | 0.24139 | 0.0 | 98.30 +Neigh | 0.0027068 | 0.0027068 | 0.0027068 | 0.0 | 1.10 +Comm | 0.00051188 | 0.00051188 | 0.00051188 | 0.0 | 0.21 +Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.04 +Modify | 0.00059605 | 0.00059605 | 0.00059605 | 0.0 | 0.24 +Other | | 0.0002608 | | | 0.11 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -196,18 +197,18 @@ Dangerous builds = 0 clear using 1 OpenMP thread(s) per MPI task -read_restart restart.equil +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 restoring atom style atomic from restart orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 seconds pair_style vashishta -pair_coeff * * InP.vashishta In In In In P P P P +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 @@ -247,20 +248,20 @@ Step Temp E_pair TotEng Econserve Press 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 0.217808 on 1 procs for 100 steps with 512 atoms +Loop time of 0.111899 on 1 procs for 100 steps with 512 atoms -Performance: 39.668 ns/day, 0.605 hours/ns, 459.121 timesteps/s -98.2% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 77.212 ns/day, 0.311 hours/ns, 893.662 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 | 0.19635 | 0.19635 | 0.19635 | 0.0 | 90.15 -Neigh | 0.01054 | 0.01054 | 0.01054 | 0.0 | 4.84 -Comm | 0.0051923 | 0.0051923 | 0.0051923 | 0.0 | 2.38 -Output | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.13 -Modify | 0.0048637 | 0.0048637 | 0.0048637 | 0.0 | 2.23 -Other | | 0.0005858 | | | 0.27 +Pair | 0.10539 | 0.10539 | 0.10539 | 0.0 | 94.18 +Neigh | 0.0049229 | 0.0049229 | 0.0049229 | 0.0 | 4.40 +Comm | 0.00068307 | 0.00068307 | 0.00068307 | 0.0 | 0.61 +Output | 6.1989e-05 | 6.1989e-05 | 6.1989e-05 | 0.0 | 0.06 +Modify | 0.00058532 | 0.00058532 | 0.00058532 | 0.0 | 0.52 +Other | | 0.0002604 | | | 0.23 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -280,28 +281,28 @@ Dangerous builds = 0 clear using 1 OpenMP thread(s) per MPI task -read_restart restart.equil +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 restoring atom style atomic from restart orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 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 +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 +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 @@ -341,20 +342,20 @@ Step Temp E_pair TotEng Econserve Press 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 0.487425 on 1 procs for 100 steps with 512 atoms +Loop time of 0.097734 on 1 procs for 100 steps with 512 atoms -Performance: 17.726 ns/day, 1.354 hours/ns, 205.160 timesteps/s -99.1% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 88.403 ns/day, 0.271 hours/ns, 1023.186 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.47762 | 0.47762 | 0.47762 | 0.0 | 97.99 -Neigh | 0.0014286 | 0.0014286 | 0.0014286 | 0.0 | 0.29 -Comm | 0.0024068 | 0.0024068 | 0.0024068 | 0.0 | 0.49 -Output | 0.00028992 | 0.00028992 | 0.00028992 | 0.0 | 0.06 -Modify | 0.0050635 | 0.0050635 | 0.0050635 | 0.0 | 1.04 -Other | | 0.0006182 | | | 0.13 +Pair | 0.095481 | 0.095481 | 0.095481 | 0.0 | 97.69 +Neigh | 0.000772 | 0.000772 | 0.000772 | 0.0 | 0.79 +Comm | 0.00046158 | 0.00046158 | 0.00046158 | 0.0 | 0.47 +Output | 6.7949e-05 | 6.7949e-05 | 6.7949e-05 | 0.0 | 0.07 +Modify | 0.00068784 | 0.00068784 | 0.00068784 | 0.0 | 0.70 +Other | | 0.0002635 | | | 0.27 Nlocal: 512.000 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -370,4 +371,99 @@ Ave neighs/atom = 28.523438 Neighbor list builds = 1 Dangerous builds = 0 +# Test Tersoff/ZBL model for SiC + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil +Reading restart file ... + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 + restoring atom style atomic from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + read_restart CPU = 0.000 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/zbl +pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si +Reading tersoff/zbl potential file SiC.tersoff.zbl with DATE: 2009-04-15 + +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 = 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 diff --git a/examples/threebody/log.08Feb21.threebody.g++.4 b/examples/threebody/log.29Sep21.threebody.g++.4 similarity index 52% rename from examples/threebody/log.08Feb21.threebody.g++.4 rename to examples/threebody/log.29Sep21.threebody.g++.4 index f747be509d..da745502eb 100644 --- a/examples/threebody/log.08Feb21.threebody.g++.4 +++ b/examples/threebody/log.29Sep21.threebody.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (24 Dec 2020) +LAMMPS (29 Sep 2021 - Update 3) using 1 OpenMP thread(s) per MPI task # Simple regression tests for threebody potentials @@ -9,7 +9,7 @@ units metal atom_style atomic atom_modify map array boundary p p p -atom_modify sort 0 0.0 +atom_modify sort 0 0.0 # temperature @@ -26,20 +26,21 @@ region myreg block 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 + 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 - create_atoms CPU = 0.074 seconds + using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) + create_atoms CPU = 0.000 seconds mass * 28.06 -velocity all create $t 5287287 loop geom -velocity all create 1800 5287287 loop geom +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 +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 @@ -63,7 +64,7 @@ Neighbor list info ... 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 +Per MPI rank memory allocation (min/avg/max) = 2.983 | 2.983 | 2.983 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 @@ -76,54 +77,54 @@ Step Temp E_pair TotEng Econserve Press 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 +Loop time of 0.089642 on 1 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 +Performance: 96.383 ns/day, 0.249 hours/ns, 1115.548 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.037337 | 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 +Pair | 0.086619 | 0.086619 | 0.086619 | 0.0 | 96.63 +Neigh | 0.0015211 | 0.0015211 | 0.0015211 | 0.0 | 1.70 +Comm | 0.000458 | 0.000458 | 0.000458 | 0.0 | 0.51 +Output | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 0.09 +Modify | 0.00073361 | 0.00073361 | 0.00073361 | 0.0 | 0.82 +Other | | 0.0002301 | | | 0.26 -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 +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1017.00 ave 1017 max 1017 min +Histogram: 1 0 0 0 0 0 0 0 0 0 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 +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 13988.0 ave 13988 max 13988 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13988 Ave neighs/atom = 27.320312 Neighbor list builds = 2 Dangerous builds = 0 -write_restart restart.equil +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 +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 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 + 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 seconds pair_style sw -pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te +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 @@ -150,42 +151,42 @@ Neighbor list info ... 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 +Per MPI rank memory allocation (min/avg/max) = 3.001 | 3.001 | 3.001 Mbytes Step Temp E_pair TotEng Econserve Press - 100 1112.9699 -625.76163 -552.24782 -564.38354 462129.66 + 100 1112.9699 -625.76163 -552.24781 -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 + 120 1926.4523 -674.71265 -547.46675 -564.53612 486338.88 + 130 1152.6663 -621.47264 -545.33681 -564.37203 514892.2 140 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 + 150 1767.8665 -657.67178 -540.90078 -564.48386 466721.31 + 160 1075.2874 -610.12809 -539.10328 -564.36709 470151.9 + 170 1697.9313 -649.3684 -537.21675 -564.47207 467953.71 + 180 1856.1197 -657.14338 -534.54309 -564.48754 488372.27 + 190 1346.1107 -621.42431 -532.5111 -564.38065 511750.04 200 1919.5266 -657.26587 -530.47743 -564.47797 488684.56 -Loop time of 0.286556 on 4 procs for 100 steps with 512 atoms +Loop time of 0.268183 on 1 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 +Performance: 32.217 ns/day, 0.745 hours/ns, 372.880 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.11093 | 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 +Pair | 0.26374 | 0.26374 | 0.26374 | 0.0 | 98.34 +Neigh | 0.0027301 | 0.0027301 | 0.0027301 | 0.0 | 1.02 +Comm | 0.00063014 | 0.00063014 | 0.00063014 | 0.0 | 0.23 +Output | 8.4639e-05 | 8.4639e-05 | 8.4639e-05 | 0.0 | 0.03 +Modify | 0.00072742 | 0.00072742 | 0.00072742 | 0.0 | 0.27 +Other | | 0.0002725 | | | 0.10 -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 +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1428.00 ave 1428 max 1428 min +Histogram: 1 0 0 0 0 0 0 0 0 0 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 +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 17344.0 ave 17344 max 17344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17344 Ave neighs/atom = 33.875000 @@ -196,18 +197,18 @@ Dangerous builds = 0 clear using 1 OpenMP thread(s) per MPI task -read_restart restart.equil +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 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 + 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.001 seconds + read_restart CPU = 0.000 seconds pair_style vashishta -pair_coeff * * InP.vashishta In In In In P P P P +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 @@ -234,7 +235,7 @@ Neighbor list info ... 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 +Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 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 @@ -247,29 +248,29 @@ Step Temp E_pair TotEng Econserve Press 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 +Loop time of 0.117875 on 1 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 +Performance: 73.298 ns/day, 0.327 hours/ns, 848.357 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.047903 | 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 +Pair | 0.11085 | 0.11085 | 0.11085 | 0.0 | 94.04 +Neigh | 0.005235 | 0.005235 | 0.005235 | 0.0 | 4.44 +Comm | 0.00077152 | 0.00077152 | 0.00077152 | 0.0 | 0.65 +Output | 7.9155e-05 | 7.9155e-05 | 7.9155e-05 | 0.0 | 0.07 +Modify | 0.00065637 | 0.00065637 | 0.00065637 | 0.0 | 0.56 +Other | | 0.0002811 | | | 0.24 -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 +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1838.00 ave 1838 max 1838 min +Histogram: 1 0 0 0 0 0 0 0 0 0 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 +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 36482.0 ave 36482 max 36482 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36482 Ave neighs/atom = 71.253906 @@ -280,28 +281,28 @@ Dangerous builds = 0 clear using 1 OpenMP thread(s) per MPI task -read_restart restart.equil +read_restart restart.equil Reading restart file ... - restart file = 24 Dec 2020, LAMMPS = 24 Dec 2020 + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 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 + 1 by 1 by 1 MPI processor grid pair style sw stores no restart info 512 atoms - read_restart CPU = 0.005 seconds + read_restart CPU = 0.000 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 +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 +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 @@ -328,7 +329,7 @@ Neighbor list info ... 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 +Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 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 @@ -341,33 +342,128 @@ Step Temp E_pair TotEng Econserve Press 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 +Loop time of 0.098053 on 1 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 +Performance: 88.116 ns/day, 0.272 hours/ns, 1019.857 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.13281 | 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 +Pair | 0.096055 | 0.096055 | 0.096055 | 0.0 | 97.96 +Neigh | 0.00079703 | 0.00079703 | 0.00079703 | 0.0 | 0.81 +Comm | 0.00034523 | 0.00034523 | 0.00034523 | 0.0 | 0.35 +Output | 6.8903e-05 | 6.8903e-05 | 6.8903e-05 | 0.0 | 0.07 +Modify | 0.00060797 | 0.00060797 | 0.00060797 | 0.0 | 0.62 +Other | | 0.0001793 | | | 0.18 -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 +Nlocal: 512.000 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1028.00 ave 1028 max 1028 min +Histogram: 1 0 0 0 0 0 0 0 0 0 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 +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 14604.0 ave 14604 max 14604 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14604 Ave neighs/atom = 28.523438 Neighbor list builds = 1 Dangerous builds = 0 +# Test Tersoff/ZBL model for SiC + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil +Reading restart file ... + restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021 + restoring atom style atomic from restart + orthogonal box = (0.0000000 0.0000000 0.0000000) to (21.724000 21.724000 21.724000) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + read_restart CPU = 0.000 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/zbl +pair_coeff * * SiC.tersoff.zbl C C C C Si Si Si Si +Reading tersoff/zbl potential file SiC.tersoff.zbl with DATE: 2009-04-15 + +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 = 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 0.810948 on 1 procs for 100 steps with 512 atoms + +Performance: 10.654 ns/day, 2.253 hours/ns, 123.312 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 | 0.8082 | 0.8082 | 0.8082 | 0.0 | 99.66 +Neigh | 0.001195 | 0.001195 | 0.001195 | 0.0 | 0.15 +Comm | 0.00054765 | 0.00054765 | 0.00054765 | 0.0 | 0.07 +Output | 0.0001018 | 0.0001018 | 0.0001018 | 0.0 | 0.01 +Modify | 0.00062656 | 0.00062656 | 0.00062656 | 0.0 | 0.08 +Other | | 0.0002768 | | | 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