forked from lijiext/lammps
101 lines
3.3 KiB
Groff
101 lines
3.3 KiB
Groff
LAMMPS (27 Nov 2018)
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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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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000408888 secs
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mass 1 1.0
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velocity all create 3.0 87287
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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python end_of_step_callback here """
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from __future__ import print_function
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from lammps import lammps
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def end_of_step_callback(lmp):
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L = lammps(ptr=lmp)
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t = L.extract_global("ntimestep", 0)
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print("### END OF STEP ###", t)
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def post_force_callback(lmp, v):
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L = lammps(ptr=lmp)
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t = L.extract_global("ntimestep", 0)
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print("### POST_FORCE ###", t)
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"""
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fix 1 all nve
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fix 2 all python/invoke 50 end_of_step end_of_step_callback
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fix 3 all python/invoke 50 post_force post_force_callback
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#dump id all atom 50 dump.melt
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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.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 12 12 12
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
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100 1.6503357 -4.756014 0 -2.2811293 5.8050524
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150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
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200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
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250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
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Loop time of 0.227907 on 4 procs for 250 steps with 4000 atoms
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Performance: 473877.870 tau/day, 1096.940 timesteps/s
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97.4% 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 | 0.15923 | 0.16507 | 0.17227 | 1.2 | 72.43
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Neigh | 0.02438 | 0.025177 | 0.025757 | 0.4 | 11.05
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Comm | 0.022418 | 0.030157 | 0.036685 | 2.9 | 13.23
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Output | 0.00052595 | 0.00092125 | 0.0011675 | 0.0 | 0.40
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Modify | 0.0053911 | 0.0057266 | 0.006294 | 0.5 | 2.51
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Other | | 0.0008523 | | | 0.37
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Nlocal: 1000 ave 1010 max 982 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 2703.75 ave 2713 max 2689 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Neighs: 37915.5 ave 39239 max 36193 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Total # of neighbors = 151662
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Ave neighs/atom = 37.9155
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Neighbor list builds = 12
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Dangerous builds not checked
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Total wall time: 0:00:00
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