89 lines
3.6 KiB
Groff
89 lines
3.6 KiB
Groff
LAMMPS (4 May 2022)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style atomic
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# data file with one atom type
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read_data data.spce
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Reading data file ...
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orthogonal box = (0 0 0) to (31.0648 31.0648 31.0648)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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1000 atoms
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read_data CPU = 0.001 seconds
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pair_style hybrid/overlay table linear 1200 threebody/table
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#pair coefficients
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pair_coeff 1 1 table table_CG_CG.txt VOTCA
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pair_coeff * * threebody/table spce.3b type
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fix 1 all nvt temp 300.0 300.0 200.0
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velocity all create 300 432567 dist uniform loop geom mom yes
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timestep 2.0
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thermo 100
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#dump 2 all custom 100 dump.spce id type x y z fx fy fz
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run 1000
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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 = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair table, perpetual, half/full from (2)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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(2) pair threebody/table, 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) = 3.87 | 3.87 | 3.87 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 300 -5377.8719 0 -4484.5232 -320.10184
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100 296.01121 -5418.505 0 -4537.0342 -223.39972
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200 295.27654 -5430.3033 0 -4551.0202 794.29126
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300 302.16526 -5445.8048 0 -4546.0083 -11.568299
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400 308.59003 -5434.7181 0 -4515.7896 1.7337642
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500 295.346 -5436.0896 0 -4556.5996 778.73304
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600 293.14648 -5422.6082 0 -4549.6681 -148.67071
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700 307.6975 -5465.3018 0 -4549.0312 287.70203
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800 314.09436 -5467.6073 0 -4532.2879 522.73489
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900 300.85843 -5503.7551 0 -4607.85 491.78041
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1000 302.84638 -5468.3331 0 -4566.5083 338.05123
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Loop time of 1.60997 on 4 procs for 1000 steps with 1000 atoms
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Performance: 107.331 ns/day, 0.224 hours/ns, 621.131 timesteps/s
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94.2% 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 | 1.28 | 1.2942 | 1.3018 | 0.8 | 80.38
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Neigh | 0.069763 | 0.070222 | 0.070788 | 0.2 | 4.36
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Comm | 0.19379 | 0.20979 | 0.23226 | 3.6 | 13.03
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Output | 0.0001711 | 0.00046947 | 0.0013621 | 0.0 | 0.03
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Modify | 0.021613 | 0.030016 | 0.038718 | 4.8 | 1.86
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Other | | 0.005309 | | | 0.33
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Nlocal: 250 ave 257 max 240 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Nghost: 3488.75 ave 3504 max 3478 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 47828 ave 49169 max 45782 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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FullNghs: 95656 ave 98253 max 91425 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 382624
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Ave neighs/atom = 382.624
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Neighbor list builds = 27
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Dangerous builds = 0
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Total wall time: 0:00:01
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