a bunch refactoring changes in the python pair style and the examples
- make all python potential classes derived from LAMMPSPairPotential which contains shared functionality. We currently don't check for supported atom types. may want to add that again later. - keep track of skipped atom types in the C++ code. - add test against units setting. must set self.units='...' in constructor - make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force. - rename potentials.py to py_pot.py - update test runs. some small tweaks.
This commit is contained in:
Axel Kohlmeyer
178
examples/python/log.4May17.pair_python_coulomb.g++.1
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178
examples/python/log.4May17.pair_python_coulomb.g++.1
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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 coul/long 12.0 python 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 py_pot.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 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 python, 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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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 7.63869 on 1 procs for 100 steps with 4500 atoms
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Performance: 1.131 ns/day, 21.219 hours/ns, 13.091 timesteps/s
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99.6% 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 | 5.7777 | 5.7777 | 5.7777 | 0.0 | 75.64
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Bond | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00
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Kspace | 1.5385 | 1.5385 | 1.5385 | 0.0 | 20.14
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Neigh | 0.22962 | 0.22962 | 0.22962 | 0.0 | 3.01
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Comm | 0.024123 | 0.024123 | 0.024123 | 0.0 | 0.32
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Output | 0.00061131 | 0.00061131 | 0.00061131 | 0.0 | 0.01
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Modify | 0.062444 | 0.062444 | 0.062444 | 0.0 | 0.82
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Other | | 0.005466 | | | 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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