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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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46
examples/python/log.4May17.pair_python_table.g++.1
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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 1000 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) = 3.184 | 3.184 | 3.184 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733675 0 -2.2744925 -3.7033435
50 1.6758875 -4.7951764 0 -2.2819736 5.6705794
100 1.6458266 -4.7488945 0 -2.2807717 5.8696895
150 1.6324439 -4.7283321 0 -2.2802784 5.9594952
200 1.6630547 -4.7746809 0 -2.2807225 5.7372657
250 1.6278968 -4.7226363 0 -2.2814016 5.9559236
Loop time of 1.0498 on 1 procs for 250 steps with 4000 atoms
0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.6758731 -4.7953067 0 -2.2821255 5.6706553
100 1.6458118 -4.7490281 0 -2.2809276 5.8697466
150 1.632425 -4.7284533 0 -2.2804279 5.9595684
200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
Loop time of 0.996652 on 1 procs for 250 steps with 4000 atoms
Performance: 102877.190 tau/day, 238.142 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 108362.785 tau/day, 250.840 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93242 | 0.93242 | 0.93242 | 0.0 | 88.82
Neigh | 0.088495 | 0.088495 | 0.088495 | 0.0 | 8.43
Comm | 0.012153 | 0.012153 | 0.012153 | 0.0 | 1.16
Output | 0.00013924 | 0.00013924 | 0.00013924 | 0.0 | 0.01
Modify | 0.013729 | 0.013729 | 0.013729 | 0.0 | 1.31
Other | | 0.002855 | | | 0.27
Pair | 0.87999 | 0.87999 | 0.87999 | 0.0 | 88.29
Neigh | 0.087921 | 0.087921 | 0.087921 | 0.0 | 8.82
Comm | 0.012098 | 0.012098 | 0.012098 | 0.0 | 1.21
Output | 0.00013614 | 0.00013614 | 0.00013614 | 0.0 | 0.01
Modify | 0.01363 | 0.01363 | 0.01363 | 0.0 | 1.37
Other | | 0.002882 | | | 0.29
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5504 ave 5504 max 5504 min
Nghost: 5500 ave 5500 max 5500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151497 ave 151497 max 151497 min
Neighs: 151496 ave 151496 max 151496 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151497
Ave neighs/atom = 37.8743
Total # of neighbors = 151496
Ave neighs/atom = 37.874
Neighbor list builds = 12
Dangerous builds not checked