43efe9e417
with the single function, python pair styles can be massively sped up and made compatible to accelerators, as one can translate the analytic force and energy functions through LAMMPS into suitable tables and then simply use the on-the-fly tables for production runs
179 lines
6.1 KiB
Groff
179 lines
6.1 KiB
Groff
LAMMPS (4 May 2017)
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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 hybrid/overlay python 12.0 coul/long 12.0
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kspace_style pppm 1.0e-6
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pair_coeff * * coul/long
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pair_coeff * * python potentials.LJCutSPCE OW NULL
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pair_modify table 0
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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 combined lj/coul table for all atom types
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../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 = 0.000394206
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estimated relative force accuracy = 1.18714e-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 python, perpetual, skip from (2)
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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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(2) 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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pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../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 = 0.000394206
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estimated relative force accuracy = 1.18714e-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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pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
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PPPM initialization ...
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WARNING: Using polynomial approximation for long-range coulomb (../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 = 0.000394206
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estimated relative force accuracy = 1.18714e-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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# switch to tabulated potential
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pair_style table linear 2000 pppm
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pair_coeff 1 1 spce.table OW-OW
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pair_coeff 1 2 spce.table OW-HW
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pair_coeff 2 2 spce.table HW-HW
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thermo 10
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run 100
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../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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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, 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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Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -100272.97 0 -100272.97 -1282.0708
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10 120.61568 -101350.63 0 -100272.39 -4077.5051
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20 136.11379 -101465.43 0 -100248.65 -5136.5677
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30 137.01602 -101455.3 0 -100230.46 -5347.8311
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40 153.424 -101582.46 0 -100210.93 -5223.1676
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50 167.73654 -101686.24 0 -100186.77 -4468.6687
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60 163.11642 -101618.16 0 -100159.99 -3291.7815
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70 169.64512 -101647.89 0 -100131.35 -2611.638
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80 182.9979 -101737.01 0 -100101.11 -2390.6293
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90 191.33873 -101778.71 0 -100068.24 -2239.386
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100 194.7458 -101775.84 0 -100034.92 -1951.9128
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Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
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Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
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99.7% 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 | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51
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Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00
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Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24
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Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02
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Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32
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Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01
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Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83
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Other | | 0.005243 | | | 0.07
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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 = 2601766
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Ave neighs/atom = 578.17
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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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