forked from lijiext/lammps
149 lines
5.1 KiB
Groff
149 lines
5.1 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style python 12.0
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pair_coeff * * py_pot.LJCutSPCE OW HW
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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# create only lj/cut table for the oxygen atoms from python
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shell rm -f spce.table
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WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
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WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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# switch to tabulated potential with long-range coulomb as overlay
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pair_style hybrid/overlay coul/long 12.0 table linear 2000
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kspace_style pppm 1.0e-6
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pair_coeff * * coul/long
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pair_coeff 1 1 table spce.table OW-OW
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WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (src/pair_table.cpp:481)
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thermo 10
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 103823 64000
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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) pair table, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 36.57 | 36.57 | 36.57 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -16690.019 0 -16690.019 -1268.9124
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10 120.58553 -17767.489 0 -16689.521 -4063.8136
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20 136.11736 -17882.538 0 -16665.724 -5124.6194
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30 137.00764 -17872.302 0 -16647.529 -5337.1515
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40 153.38867 -17999.256 0 -16628.046 -5213.5616
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50 167.70342 -18103.046 0 -16603.87 -4460.6216
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60 163.07134 -18034.842 0 -16577.074 -3284.9621
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70 169.59286 -18064.622 0 -16548.556 -2606.3642
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80 182.92892 -18153.485 0 -16518.202 -2385.4747
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90 191.2793 -18195.343 0 -16485.411 -2235.3292
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100 194.68587 -18192.446 0 -16452.061 -1948.3379
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Loop time of 7.00522 on 1 procs for 100 steps with 4500 atoms
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Performance: 1.233 ns/day, 19.459 hours/ns, 14.275 timesteps/s
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98.3% 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 | 5.5664 | 5.5664 | 5.5664 | 0.0 | 79.46
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Bond | 0.00011444 | 0.00011444 | 0.00011444 | 0.0 | 0.00
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Kspace | 1.0814 | 1.0814 | 1.0814 | 0.0 | 15.44
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Neigh | 0.28011 | 0.28011 | 0.28011 | 0.0 | 4.00
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Comm | 0.020573 | 0.020573 | 0.020573 | 0.0 | 0.29
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Output | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
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Modify | 0.052692 | 0.052692 | 0.052692 | 0.0 | 0.75
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Other | | 0.003407 | | | 0.05
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 21216 ave 21216 max 21216 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2601768
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Ave neighs/atom = 578.171
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Ave special neighs/atom = 2
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Neighbor list builds = 3
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Dangerous builds = 0
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shell rm spce.table
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Total wall time: 0:00:07
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