jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/examples/python/log.4May17.pair_python_hybr...

248 lines
8.2 KiB
Groff
Raw Normal View History

provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
update log files in python pair style example
2017-05-17 20:00:21 +08:00
1 by 2 by 2 MPI processor grid
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
create_atoms 1 box
Created 4000 atoms
mass * 1.0
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
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.LJCutMelt lj NULL
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
update log files in python pair style example
2017-05-17 20:00:21 +08:00
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
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
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
Loop time of 6.01723 on 4 procs for 250 steps with 4000 atoms
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
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
Performance: 17948.472 tau/day, 41.547 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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 | 5.1507 | 5.4989 | 5.9629 | 13.1 | 91.39
Neigh | 0.024123 | 0.024877 | 0.025959 | 0.5 | 0.41
Comm | 0.02258 | 0.48785 | 0.83691 | 44.1 | 8.11
Output | 0.00039768 | 0.00045246 | 0.00052929 | 0.0 | 0.01
Modify | 0.0036325 | 0.0037773 | 0.0038905 | 0.2 | 0.06
Other | | 0.001357 | | | 0.02
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Nlocal: 1000 ave 1010 max 982 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
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Neighs: 0 ave 0 max 0 min
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Histogram: 4 0 0 0 0 0 0 0 0 0
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
write_data hybrid.data
write_restart hybrid.restart
clear
using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
update log files in python pair style example
2017-05-17 20:00:21 +08:00
1 by 2 by 2 MPI processor grid
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5
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.LJCutMelt lj NULL
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Step Temp E_pair E_mol TotEng Press
update log files in python pair style example
2017-05-17 20:00:21 +08:00
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
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
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
Loop time of 6.09991 on 4 procs for 250 steps with 4000 atoms
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
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
Performance: 17705.179 tau/day, 40.984 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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 | 5.2315 | 5.5179 | 6.0183 | 13.7 | 90.46
Neigh | 0.049134 | 0.051424 | 0.053837 | 0.8 | 0.84
Comm | 0.021671 | 0.52455 | 0.8132 | 44.5 | 8.60
Output | 0.00019336 | 0.00026017 | 0.00032115 | 0.0 | 0.00
Modify | 0.0036032 | 0.0036635 | 0.0038021 | 0.1 | 0.06
Other | | 0.002068 | | | 0.03
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2699 ave 2706 max 2693 min
Histogram: 1 1 0 0 0 0 1 0 0 1
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Neighs: 0 ave 0 max 0 min
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Histogram: 4 0 0 0 0 0 0 0 0 0
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 25
Dangerous builds = 25
clear
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data hybrid.data
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
update log files in python pair style example
2017-05-17 20:00:21 +08:00
1 by 2 by 2 MPI processor grid
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
reading atoms ...
4000 atoms
reading velocities ...
4000 velocities
pair_style hybrid lj/cut 2.5 python 2.5
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.LJCutMelt lj NULL
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Step Temp E_pair E_mol TotEng Press
update log files in python pair style example
2017-05-17 20:00:21 +08:00
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
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
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
Loop time of 6.04476 on 4 procs for 250 steps with 4000 atoms
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
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
Performance: 17866.705 tau/day, 41.358 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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 | 5.2589 | 5.5841 | 5.9788 | 11.1 | 92.38
Neigh | 0.023942 | 0.024705 | 0.025509 | 0.4 | 0.41
Comm | 0.034946 | 0.43056 | 0.75671 | 40.0 | 7.12
Output | 0.00022149 | 0.00029725 | 0.0003593 | 0.0 | 0.00
Modify | 0.003613 | 0.0037647 | 0.003829 | 0.1 | 0.06
Other | | 0.001313 | | | 0.02
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 2695.5 ave 2706 max 2682 min
Histogram: 1 0 0 0 0 0 2 0 0 1
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Neighs: 0 ave 0 max 0 min
update log files in python pair style example
2017-05-17 20:00:21 +08:00
Histogram: 4 0 0 0 0 0 0 0 0 0
provide reference output for python pair style inputs
2017-05-15 12:25:11 +08:00
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
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 wall time: 0:00:18