67962b15fc
- 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.
100 lines
3.3 KiB
Groff
100 lines
3.3 KiB
Groff
LAMMPS (4 May 2017)
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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 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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mass * 1.0
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velocity all create 3.0 87287
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
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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 = 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 python, 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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pair_style table linear 2000
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pair_coeff 1 1 lj_1_1.table LJ
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WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (../pair_table.cpp:476)
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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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 table, 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) = 3.184 | 3.184 | 3.184 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733629 0 -2.2744879 -3.7032813
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50 1.6758731 -4.7953067 0 -2.2821255 5.6706553
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100 1.6458118 -4.7490281 0 -2.2809276 5.8697466
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150 1.632425 -4.7284533 0 -2.2804279 5.9595684
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200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
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250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
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Loop time of 0.996652 on 1 procs for 250 steps with 4000 atoms
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Performance: 108362.785 tau/day, 250.840 timesteps/s
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99.8% 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 | 0.87999 | 0.87999 | 0.87999 | 0.0 | 88.29
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Neigh | 0.087921 | 0.087921 | 0.087921 | 0.0 | 8.82
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Comm | 0.012098 | 0.012098 | 0.012098 | 0.0 | 1.21
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Output | 0.00013614 | 0.00013614 | 0.00013614 | 0.0 | 0.01
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Modify | 0.01363 | 0.01363 | 0.01363 | 0.0 | 1.37
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Other | | 0.002882 | | | 0.29
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Nlocal: 4000 ave 4000 max 4000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 5500 ave 5500 max 5500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 151496 ave 151496 max 151496 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 151496
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Ave neighs/atom = 37.874
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Neighbor list builds = 12
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Dangerous builds not checked
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shell rm lj_1_1.table
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Total wall time: 0:00:01
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