236 lines
12 KiB
Groff
236 lines
12 KiB
Groff
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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processors * 1 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 10 0 10 0 10
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create_box 3 box
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Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
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4 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
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create_atoms CPU = 0.000 seconds
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mass * 1.0
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region long block 3 6 0 10 0 10
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set region long type 2
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Setting atom values ...
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1400 settings made for type
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velocity all create 1.0 87287
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_coeff * 2 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify every 2 delay 4 check yes
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fix p all property/atom d_WEIGHT
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fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT
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compute p all property/atom d_WEIGHT
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variable maximb equal f_0[1]
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variable iter equal f_0[2]
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variable prev equal f_0[3]
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variable final equal f_0
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#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump id all custom 50 dump.lammpstrj id type x y z c_p
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
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thermo 50
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 2 steps, delay = 4 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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WARNING: Balance weight neigh skipped b/c no suitable list found (src/imbalance_neigh.cpp:65)
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Per MPI rank memory allocation (min/avg/max) = 3.692 | 4.073 | 4.455 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
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50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137
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100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137
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150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137
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200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137
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250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137
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300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137
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350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137
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400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137
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450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137
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500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
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Loop time of 1.55023 on 4 procs for 500 steps with 4000 atoms
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Performance: 139333.812 tau/day, 322.532 timesteps/s, 1.290 Matom-step/s
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98.7% CPU use with 4 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 | 0.71992 | 0.87383 | 0.98696 | 11.0 | 56.37
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Neigh | 0.21071 | 0.30874 | 0.44041 | 17.8 | 19.92
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Comm | 0.32187 | 0.35451 | 0.38467 | 4.4 | 22.87
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Output | 0.00037371 | 0.00042 | 0.00044758 | 0.0 | 0.03
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Modify | 0.0049391 | 0.0063638 | 0.0082893 | 1.8 | 0.41
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Other | | 0.006361 | | | 0.41
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Nlocal: 1000 ave 1549 max 605 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8755 ave 9851 max 8071 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 149308 ave 164554 max 128538 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 597231
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Ave neighs/atom = 149.30775
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Neighbor list builds = 50
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Dangerous builds = 0
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.099 | 4.288 | 4.477 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137
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550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137
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600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137
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650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137
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700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137
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750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137
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800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137
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850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137
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900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137
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950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137
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1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
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Loop time of 1.67278 on 4 procs for 500 steps with 4000 atoms
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Performance: 129126.174 tau/day, 298.903 timesteps/s, 1.196 Matom-step/s
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99.1% CPU use with 4 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 | 0.84049 | 0.96125 | 1.0434 | 8.0 | 57.46
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Neigh | 0.23438 | 0.35614 | 0.5167 | 20.4 | 21.29
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Comm | 0.28073 | 0.34108 | 0.41025 | 9.1 | 20.39
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Output | 0.00039366 | 0.00043302 | 0.00046464 | 0.0 | 0.03
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Modify | 0.0050479 | 0.006849 | 0.0091921 | 2.2 | 0.41
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Other | | 0.007028 | | | 0.42
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Nlocal: 1000 ave 1569 max 595 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8715.25 ave 9779 max 8018 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 150170 ave 163282 max 132114 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 600678
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Ave neighs/atom = 150.1695
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Neighbor list builds = 53
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Dangerous builds = 0
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.099 | 4.288 | 4.477 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137
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1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137
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1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137
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1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137
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1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137
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1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137
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1300 0.54134321 -6.2590728 0 -5.447261 -1.9170271 4738.2137
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1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137
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1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137
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1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137
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1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
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Loop time of 1.66639 on 4 procs for 500 steps with 4000 atoms
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Performance: 129621.198 tau/day, 300.049 timesteps/s, 1.200 Matom-step/s
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99.1% CPU use with 4 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 | 0.8486 | 0.96611 | 1.1004 | 9.8 | 57.98
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Neigh | 0.22624 | 0.34016 | 0.49564 | 19.9 | 20.41
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Comm | 0.3065 | 0.34614 | 0.41937 | 7.4 | 20.77
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Output | 0.00040364 | 0.00043928 | 0.00051275 | 0.0 | 0.03
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Modify | 0.0049921 | 0.0067008 | 0.008971 | 2.1 | 0.40
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Other | | 0.00684 | | | 0.41
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Nlocal: 1000 ave 1543 max 605 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8704.5 ave 9803 max 7983 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 150494 ave 166334 max 129306 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 601974
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Ave neighs/atom = 150.4935
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.099 | 4.288 | 4.477 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137
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1550 0.55327018 -6.2750126 0 -5.4453148 -1.9506585 4738.2137
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1600 0.54419004 -6.2612622 0 -5.4451812 -1.8559437 4738.2137
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1650 0.54710034 -6.2661938 0 -5.4457484 -1.8882763 4738.2137
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1700 0.53665691 -6.2504958 0 -5.4457117 -1.8068009 4738.2137
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1750 0.5486471 -6.2681127 0 -5.4453478 -1.8662656 4738.2137
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1800 0.54476222 -6.2615086 0 -5.4445695 -1.8352838 4738.2137
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1850 0.54143048 -6.2555517 0 -5.443609 -1.8005726 4738.2137
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1900 0.53992511 -6.254136 0 -5.4444508 -1.7768715 4738.2137
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1950 0.54665895 -6.2640958 0 -5.4443124 -1.7946993 4738.2137
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2000 0.5455751 -6.2625337 0 -5.4443756 -1.8072242 4738.2137
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Loop time of 1.69092 on 4 procs for 500 steps with 4000 atoms
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Performance: 127741.463 tau/day, 295.698 timesteps/s, 1.183 Matom-step/s
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99.1% CPU use with 4 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 | 0.85108 | 0.9612 | 1.0789 | 9.0 | 56.85
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Neigh | 0.2452 | 0.37468 | 0.5456 | 20.7 | 22.16
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Comm | 0.27839 | 0.34103 | 0.42333 | 9.0 | 20.17
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Output | 0.00038835 | 0.00042678 | 0.00046578 | 0.0 | 0.03
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Modify | 0.0049259 | 0.0067032 | 0.0090783 | 2.2 | 0.40
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Other | | 0.006874 | | | 0.41
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Nlocal: 1000 ave 1539 max 607 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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Nghost: 8677 ave 9837 max 7981 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Neighs: 151655 ave 168263 max 129443 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 606619
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Ave neighs/atom = 151.65475
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Neighbor list builds = 56
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Dangerous builds = 0
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Total wall time: 0:00:06
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