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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_hybrid.g++.1
View File

@ -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 hybrid
@ -19,7 +18,7 @@ mass * 1.0
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python potentials.LJCutMelt lj NULL
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
@ -59,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 43.2436 on 1 procs for 250 steps with 4000 atoms
Loop time of 21.9463 on 1 procs for 250 steps with 4000 atoms
Performance: 2497.477 tau/day, 5.781 timesteps/s
31.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 4921.114 tau/day, 11.391 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 42.933 | 42.933 | 42.933 | 0.0 | 99.28
Neigh | 0.24816 | 0.24816 | 0.24816 | 0.0 | 0.57
Comm | 0.027748 | 0.027748 | 0.027748 | 0.0 | 0.06
Output | 0.000519 | 0.000519 | 0.000519 | 0.0 | 0.00
Modify | 0.028028 | 0.028028 | 0.028028 | 0.0 | 0.06
Other | | 0.005912 | | | 0.01
Pair | 21.819 | 21.819 | 21.819 | 0.0 | 99.42
Neigh | 0.094718 | 0.094718 | 0.094718 | 0.0 | 0.43
Comm | 0.01407 | 0.01407 | 0.01407 | 0.0 | 0.06
Output | 0.00024915 | 0.00024915 | 0.00024915 | 0.0 | 0.00
Modify | 0.015002 | 0.015002 | 0.015002 | 0.0 | 0.07
Other | | 0.003232 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -90,7 +89,6 @@ write_data hybrid.data
write_restart hybrid.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 hybrid.restart
@ -99,7 +97,7 @@ read_restart hybrid.restart
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python potentials.LJCutMelt lj NULL
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
@ -136,20 +134,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 46.2882 on 1 procs for 250 steps with 4000 atoms
Loop time of 21.9098 on 1 procs for 250 steps with 4000 atoms
Performance: 2333.206 tau/day, 5.401 timesteps/s
31.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 4929.303 tau/day, 11.410 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.662 | 45.662 | 45.662 | 0.0 | 98.65
Neigh | 0.55234 | 0.55234 | 0.55234 | 0.0 | 1.19
Comm | 0.035614 | 0.035614 | 0.035614 | 0.0 | 0.08
Output | 0.000544 | 0.000544 | 0.000544 | 0.0 | 0.00
Modify | 0.029269 | 0.029269 | 0.029269 | 0.0 | 0.06
Other | | 0.008735 | | | 0.02
Pair | 21.68 | 21.68 | 21.68 | 0.0 | 98.95
Neigh | 0.19625 | 0.19625 | 0.19625 | 0.0 | 0.90
Comm | 0.014877 | 0.014877 | 0.014877 | 0.0 | 0.07
Output | 0.00027227 | 0.00027227 | 0.00027227 | 0.0 | 0.00
Modify | 0.013663 | 0.013663 | 0.013663 | 0.0 | 0.06
Other | | 0.004371 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -164,7 +162,6 @@ 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
@ -179,7 +176,7 @@ read_data hybrid.data
4000 velocities
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python potentials.LJCutMelt lj NULL
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
@ -219,20 +216,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 46.4094 on 1 procs for 250 steps with 4000 atoms
Loop time of 22.091 on 1 procs for 250 steps with 4000 atoms
Performance: 2327.115 tau/day, 5.387 timesteps/s
31.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 4888.868 tau/day, 11.317 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 46.066 | 46.066 | 46.066 | 0.0 | 99.26
Neigh | 0.27099 | 0.27099 | 0.27099 | 0.0 | 0.58
Comm | 0.033778 | 0.033778 | 0.033778 | 0.0 | 0.07
Output | 0.000507 | 0.000507 | 0.000507 | 0.0 | 0.00
Modify | 0.030938 | 0.030938 | 0.030938 | 0.0 | 0.07
Other | | 0.006695 | | | 0.01
Pair | 21.966 | 21.966 | 21.966 | 0.0 | 99.43
Neigh | 0.094647 | 0.094647 | 0.094647 | 0.0 | 0.43
Comm | 0.013071 | 0.013071 | 0.013071 | 0.0 | 0.06
Output | 0.00027871 | 0.00027871 | 0.00027871 | 0.0 | 0.00
Modify | 0.013882 | 0.013882 | 0.013882 | 0.0 | 0.06
Other | | 0.003102 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -247,4 +244,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:02:20
Total wall time: 0:01:07