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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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50
examples/python/log.4May17.pair_python_table.g++.4
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@ -18,10 +18,10 @@ 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
# generate tabulated potential from python variant
pair_write 1 1 10000 rsq 0.01 2.5 lj_1_1.table LJ
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -35,9 +35,9 @@ Neighbor list info ...
stencil: half/bin/3d/newton
bin: standard
pair_style table linear 10000
pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ
WARNING: 1 of 10000 force values in table are inconsistent with -dE/dr.
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476)
neighbor 0.3 bin
@ -61,36 +61,36 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733675 0 -2.2744925 -3.7033435
50 1.6754092 -4.794723 0 -2.2822376 5.6616601
100 1.6503295 -4.7559815 0 -2.2811061 5.8051261
150 1.6596603 -4.7699379 0 -2.2810699 5.7830168
200 1.6371948 -4.7365549 0 -2.2813766 5.9245585
250 1.6321199 -4.7288017 0 -2.2812339 5.9776124
Loop time of 0.313548 on 4 procs for 250 steps with 4000 atoms
0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.675395 -4.7945736 0 -2.2821094 5.6620623
100 1.6503067 -4.7558145 0 -2.2809733 5.8055967
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
200 1.6371471 -4.7363942 0 -2.2812874 5.924977
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
Loop time of 0.300176 on 4 procs for 250 steps with 4000 atoms
Performance: 344444.576 tau/day, 797.325 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 359789.395 tau/day, 832.846 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24963 | 0.25443 | 0.2632 | 1.1 | 81.15
Neigh | 0.023249 | 0.023735 | 0.024497 | 0.3 | 7.57
Comm | 0.020689 | 0.030402 | 0.035249 | 3.4 | 9.70
Output | 0.00020766 | 0.00021476 | 0.00023031 | 0.0 | 0.07
Modify | 0.0034959 | 0.0035564 | 0.0036762 | 0.1 | 1.13
Other | | 0.001206 | | | 0.38
Pair | 0.23104 | 0.23876 | 0.2451 | 1.2 | 79.54
Neigh | 0.022763 | 0.023687 | 0.024305 | 0.4 | 7.89
Comm | 0.025416 | 0.032499 | 0.041304 | 3.7 | 10.83
Output | 0.00015378 | 0.00016057 | 0.00017667 | 0.0 | 0.05
Modify | 0.0035894 | 0.0036637 | 0.0037456 | 0.1 | 1.22
Other | | 0.001409 | | | 0.47
Nlocal: 1000 ave 1010 max 982 min
Nlocal: 1000 ave 1010 max 981 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39231 max 36202 min
Nghost: 2703 ave 2715 max 2688 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 37915.2 ave 39191 max 36151 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Total # of neighbors = 151661
Ave neighs/atom = 37.9153
Neighbor list builds = 12
Dangerous builds not checked