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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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65
examples/python/log.4May17.pair_python_melt.g++.4
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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
# 3d Lennard-Jones melt
@ -19,7 +18,7 @@ mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * potentials.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
@ -48,20 +47,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 12.7083 on 4 procs for 250 steps with 4000 atoms
Loop time of 5.83903 on 4 procs for 250 steps with 4000 atoms
Performance: 8498.384 tau/day, 19.672 timesteps/s
31.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 18496.226 tau/day, 42.815 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.491 | 11.96 | 12.464 | 10.0 | 94.11
Neigh | 0.065058 | 0.065956 | 0.067066 | 0.3 | 0.52
Comm | 0.16288 | 0.66706 | 1.1373 | 42.2 | 5.25
Output | 0.000416 | 0.00085025 | 0.002121 | 0.0 | 0.01
Modify | 0.010849 | 0.011123 | 0.011321 | 0.2 | 0.09
Other | | 0.003005 | | | 0.02
Pair | 5.152 | 5.5209 | 5.7679 | 9.6 | 94.55
Neigh | 0.022809 | 0.023364 | 0.023891 | 0.3 | 0.40
Comm | 0.041927 | 0.28952 | 0.65893 | 42.2 | 4.96
Output | 0.0002389 | 0.00024772 | 0.00026727 | 0.0 | 0.00
Modify | 0.0036368 | 0.0036796 | 0.0037563 | 0.1 | 0.06
Other | | 0.001328 | | | 0.02
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@ -79,7 +78,6 @@ write_data melt.data
write_restart melt.restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
read_restart melt.restart
@ -88,7 +86,7 @@ read_restart melt.restart
4000 atoms
pair_style python 2.5
pair_coeff * * potentials.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
fix 1 all nve
@ -114,20 +112,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 12.6852 on 4 procs for 250 steps with 4000 atoms
Loop time of 5.85683 on 4 procs for 250 steps with 4000 atoms
Performance: 8513.855 tau/day, 19.708 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 18440.001 tau/day, 42.685 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.653 | 11.92 | 12.472 | 9.6 | 93.97
Neigh | 0.13284 | 0.13556 | 0.13729 | 0.5 | 1.07
Comm | 0.051389 | 0.60884 | 0.88175 | 43.0 | 4.80
Output | 0.000362 | 0.0046985 | 0.008143 | 5.1 | 0.04
Modify | 0.011007 | 0.011344 | 0.011857 | 0.3 | 0.09
Other | | 0.004278 | | | 0.03
Pair | 5.2483 | 5.5095 | 5.7744 | 8.0 | 94.07
Neigh | 0.047228 | 0.047998 | 0.049293 | 0.4 | 0.82
Comm | 0.027134 | 0.29341 | 0.55554 | 34.6 | 5.01
Output | 0.00020003 | 0.00021219 | 0.0002358 | 0.0 | 0.00
Modify | 0.0035472 | 0.0036988 | 0.0038681 | 0.2 | 0.06
Other | | 0.001984 | | | 0.03
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@ -142,7 +140,6 @@ Neighbor list builds = 25
Dangerous builds = 25
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
units lj
@ -157,7 +154,7 @@ read_data melt.data
4000 velocities
pair_style python 2.5
pair_coeff * * potentials.LJCutMelt lj
pair_coeff * * py_pot.LJCutMelt lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
@ -186,20 +183,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 12.5324 on 4 procs for 250 steps with 4000 atoms
Loop time of 5.86684 on 4 procs for 250 steps with 4000 atoms
Performance: 8617.631 tau/day, 19.948 timesteps/s
31.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 18408.545 tau/day, 42.612 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.648 | 11.918 | 12.387 | 8.3 | 95.10
Neigh | 0.064038 | 0.06537 | 0.065914 | 0.3 | 0.52
Comm | 0.065189 | 0.53362 | 0.80384 | 39.4 | 4.26
Output | 0.000346 | 0.0007525 | 0.001938 | 0.0 | 0.01
Modify | 0.011255 | 0.01155 | 0.011852 | 0.2 | 0.09
Other | | 0.002751 | | | 0.02
Pair | 5.3207 | 5.5695 | 5.8071 | 7.6 | 94.93
Neigh | 0.023073 | 0.023405 | 0.023834 | 0.2 | 0.40
Comm | 0.030558 | 0.2686 | 0.51789 | 34.7 | 4.58
Output | 0.00028825 | 0.00036758 | 0.00042987 | 0.0 | 0.01
Modify | 0.0034878 | 0.0036733 | 0.0039375 | 0.3 | 0.06
Other | | 0.001259 | | | 0.02
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@ -214,4 +211,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:00:39
Total wall time: 0:00:18