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update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
LAMMPS (27 Nov 2018)
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
pair_style hybrid/overlay coul/long 12.0 python 12.0
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
pair_coeff * * python py_pot.LJCutSPCE OW NULL
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
thermo 10
run 100
PPPM initialization ...
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394674
estimated relative force accuracy = 1.18855e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
(1) pair coul/long, perpetual
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
Per MPI rank memory allocation (min/avg/max) = 41.15 | 41.15 | 41.15 Mbytes
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222
10 120.56861 -17769.719 0 -16691.902 -4082.7098
20 136.08014 -17884.591 0 -16668.109 -5140.7824
30 136.97316 -17874.351 0 -16649.887 -5351.3571
40 153.37285 -18001.493 0 -16630.424 -5227.0601
50 167.70414 -18105.435 0 -16606.252 -4473.2089
60 163.08253 -18037.29 0 -16579.422 -3295.8963
70 169.60395 -18067.078 0 -16550.912 -2615.7026
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
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
Loop time of 15.3744 on 1 procs for 100 steps with 4500 atoms
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
Performance: 0.562 ns/day, 42.707 hours/ns, 6.504 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
Pair | 13.914 | 13.914 | 13.914 | 0.0 | 90.50
Bond | 0.00013375 | 0.00013375 | 0.00013375 | 0.0 | 0.00
Kspace | 1.0852 | 1.0852 | 1.0852 | 0.0 | 7.06
Neigh | 0.29811 | 0.29811 | 0.29811 | 0.0 | 1.94
Comm | 0.020503 | 0.020503 | 0.020503 | 0.0 | 0.13
Output | 0.00045133 | 0.00045133 | 0.00045133 | 0.0 | 0.00
Modify | 0.052513 | 0.052513 | 0.052513 | 0.0 | 0.34
Other | | 0.00348 | | | 0.02
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
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
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
Neighs: 2.60176e+06 ave 2.60176e+06 max 2.60176e+06 min
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
Histogram: 1 0 0 0 0 0 0 0 0 0
a bunch refactoring changes in the python pair style and the examples - 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.
2017-05-18 08:55:48 +08:00
Total # of neighbors = 2601762
Ave neighs/atom = 578.169
update log files for pair style python examples
2017-05-17 19:52:13 +08:00
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
update log files for peptide, peri, pour and python examples
2018-11-30 03:51:25 +08:00
Total wall time: 0:00:15