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a bunch refactoring changes in the python pair style and the examples

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- 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
2017-05-17 20:55:48 -04:00
parent 1d48f287f0
commit 67962b15fc
18 changed files with 521 additions and 316 deletions
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47
examples/python/log.4May17.pair_python_spce.g++.1
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@ -1,5 +1,4 @@
LAMMPS (4 May 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
@ -22,11 +21,11 @@ read_data data.spce
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_style hybrid/overlay python 12.0 coul/long 12.0
pair_style hybrid/overlay coul/long 12.0 python 12.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff * * python potentials.LJCutSPCE OW NULL
pair_coeff * * python py_pot.LJCutSPCE OW NULL
bond_style harmonic
angle_style harmonic
@ -68,16 +67,16 @@ Neighbor list info ...
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair python, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
(1) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222
@ -91,33 +90,33 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916
Loop time of 63.3145 on 1 procs for 100 steps with 4500 atoms
Loop time of 23.0818 on 1 procs for 100 steps with 4500 atoms
Performance: 0.136 ns/day, 175.874 hours/ns, 1.579 timesteps/s
86.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.374 ns/day, 64.116 hours/ns, 4.332 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.815 | 61.815 | 61.815 | 0.0 | 97.63
Bond | 0.000132 | 0.000132 | 0.000132 | 0.0 | 0.00
Kspace | 1.2226 | 1.2226 | 1.2226 | 0.0 | 1.93
Neigh | 0.21684 | 0.21684 | 0.21684 | 0.0 | 0.34
Comm | 0.015175 | 0.015175 | 0.015175 | 0.0 | 0.02
Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.00
Modify | 0.040088 | 0.040088 | 0.040088 | 0.0 | 0.06
Other | | 0.003896 | | | 0.01
Pair | 21.186 | 21.186 | 21.186 | 0.0 | 91.79
Bond | 0.00022054 | 0.00022054 | 0.00022054 | 0.0 | 0.00
Kspace | 1.5442 | 1.5442 | 1.5442 | 0.0 | 6.69
Neigh | 0.25672 | 0.25672 | 0.25672 | 0.0 | 1.11
Comm | 0.023787 | 0.023787 | 0.023787 | 0.0 | 0.10
Output | 0.00060248 | 0.00060248 | 0.00060248 | 0.0 | 0.00
Modify | 0.064809 | 0.064809 | 0.064809 | 0.0 | 0.28
Other | | 0.005301 | | | 0.02
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21216 ave 21216 max 21216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.44594e+06 ave 1.44594e+06 max 1.44594e+06 min
Neighs: 2.60176e+06 ave 2.60176e+06 max 2.60176e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1445935
Ave neighs/atom = 321.319
Total # of neighbors = 2601762
Ave neighs/atom = 578.169
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:01:05
Total wall time: 0:00:23