forked from lijiext/lammps
adding Pair::single() support to python pair style and examples
with the single function, python pair styles can be massively sped up and made compatible to accelerators, as one can translate the analytic force and energy functions through LAMMPS into suitable tables and then simply use the on-the-fly tables for production runs
This commit is contained in:
Axel Kohlmeyer
parent
45becfb235
commit
43efe9e417
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,45 @@
|
|||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
|
||||
pair_style hybrid/overlay python 12.0 coul/long 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python potentials.LJCutSPCE OW NULL
|
||||
|
||||
pair_modify table 0
|
||||
|
||||
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
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * potentials.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 10000 rsq 0.01 2.5 lj_1_1.table LJ
|
||||
|
||||
pair_style table linear 10000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (4 May 2017)
|
||||
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
|
||||
|
||||
pair_style hybrid/overlay python 12.0 coul/long 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python potentials.LJCutSPCE OW NULL
|
||||
|
||||
pair_modify table 0
|
||||
|
||||
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
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-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
|
||||
(1) pair python, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
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
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -100272.97 0 -100272.97 -1282.0708
|
||||
10 120.61568 -101350.63 0 -100272.39 -4077.5051
|
||||
20 136.11379 -101465.43 0 -100248.65 -5136.5677
|
||||
30 137.01602 -101455.3 0 -100230.46 -5347.8311
|
||||
40 153.424 -101582.46 0 -100210.93 -5223.1676
|
||||
50 167.73654 -101686.24 0 -100186.77 -4468.6687
|
||||
60 163.11642 -101618.16 0 -100159.99 -3291.7815
|
||||
70 169.64512 -101647.89 0 -100131.35 -2611.638
|
||||
80 182.9979 -101737.01 0 -100101.11 -2390.6293
|
||||
90 191.33873 -101778.71 0 -100068.24 -2239.386
|
||||
100 194.7458 -101775.84 0 -100034.92 -1951.9128
|
||||
Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51
|
||||
Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00
|
||||
Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24
|
||||
Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02
|
||||
Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32
|
||||
Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01
|
||||
Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83
|
||||
Other | | 0.005243 | | | 0.07
|
||||
|
||||
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
|
||||
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2601766
|
||||
Ave neighs/atom = 578.17
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:07
|
||||
|
|
@ -0,0 +1,178 @@
|
|||
LAMMPS (4 May 2017)
|
||||
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)
|
||||
2 by 2 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
|
||||
|
||||
pair_style hybrid/overlay python 12.0 coul/long 12.0
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
pair_coeff * * coul/long
|
||||
pair_coeff * * python potentials.LJCutSPCE OW NULL
|
||||
|
||||
pair_modify table 0
|
||||
|
||||
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
|
||||
|
||||
# create combined lj/coul table for all atom types
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
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
|
||||
(1) pair python, perpetual, skip from (2)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
|
||||
PPPM initialization ...
|
||||
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394206
|
||||
estimated relative force accuracy = 1.18714e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
|
||||
# switch to tabulated potential
|
||||
pair_style table linear 2000 pppm
|
||||
pair_coeff 1 1 spce.table OW-OW
|
||||
pair_coeff 1 2 spce.table OW-HW
|
||||
pair_coeff 2 2 spce.table HW-HW
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||
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 = 34263 16000
|
||||
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
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.05 | 13.05 | 13.05 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -100272.97 0 -100272.97 -1282.0708
|
||||
10 120.61568 -101350.63 0 -100272.39 -4077.5051
|
||||
20 136.11379 -101465.43 0 -100248.65 -5136.5677
|
||||
30 137.01602 -101455.3 0 -100230.46 -5347.8311
|
||||
40 153.424 -101582.46 0 -100210.93 -5223.1676
|
||||
50 167.73654 -101686.24 0 -100186.77 -4468.6687
|
||||
60 163.11642 -101618.16 0 -100159.99 -3291.7815
|
||||
70 169.64512 -101647.89 0 -100131.35 -2611.638
|
||||
80 182.9979 -101737.01 0 -100101.11 -2390.6293
|
||||
90 191.33873 -101778.71 0 -100068.24 -2239.386
|
||||
100 194.7458 -101775.84 0 -100034.92 -1951.9128
|
||||
Loop time of 2.38392 on 4 procs for 100 steps with 4500 atoms
|
||||
|
||||
Performance: 3.624 ns/day, 6.622 hours/ns, 41.948 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4377 | 1.5465 | 1.6848 | 7.3 | 64.87
|
||||
Bond | 0.00010276 | 0.00012648 | 0.0001452 | 0.0 | 0.01
|
||||
Kspace | 0.53311 | 0.66842 | 0.77484 | 10.9 | 28.04
|
||||
Neigh | 0.066 | 0.066074 | 0.066101 | 0.0 | 2.77
|
||||
Comm | 0.045355 | 0.048344 | 0.050747 | 1.0 | 2.03
|
||||
Output | 0.00042391 | 0.00044996 | 0.00052667 | 0.0 | 0.02
|
||||
Modify | 0.049891 | 0.050191 | 0.050336 | 0.1 | 2.11
|
||||
Other | | 0.003771 | | | 0.16
|
||||
|
||||
Nlocal: 1125 ave 1154 max 1092 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 12256.2 ave 12296 max 12213 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 650442 ave 678824 max 626375 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2601766
|
||||
Ave neighs/atom = 578.17
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
|
||||
shell rm spce.table
|
||||
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
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 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * potentials.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 10000 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
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
pair_style table linear 10000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
WARNING: 1 of 1000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:476)
|
||||
|
||||
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
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
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
|
||||
|
||||
Performance: 102877.190 tau/day, 238.142 timesteps/s
|
||||
99.7% 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
|
||||
|
||||
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
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151497 ave 151497 max 151497 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151497
|
||||
Ave neighs/atom = 37.8743
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
LAMMPS (4 May 2017)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
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 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style python 2.5
|
||||
pair_coeff * * potentials.LJCutMelt lj
|
||||
|
||||
# generate tabulated potential from python variant
|
||||
pair_write 1 1 10000 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
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair python, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
|
||||
pair_style table linear 10000
|
||||
pair_coeff 1 1 lj_1_1.table LJ
|
||||
WARNING: 1 of 10000 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (../pair_table.cpp:476)
|
||||
|
||||
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
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair table, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
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
|
||||
|
||||
Performance: 344444.576 tau/day, 797.325 timesteps/s
|
||||
99.1% 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
|
||||
|
||||
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
|
||||
Neighs: 37915.5 ave 39231 max 36202 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 151662
|
||||
Ave neighs/atom = 37.9155
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
|
||||
shell rm lj_1_1.table
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -35,7 +35,7 @@ using namespace LAMMPS_NS;
|
|||
|
||||
PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
||||
respa_enable = 0;
|
||||
single_enable = 0;
|
||||
single_enable = 1;
|
||||
writedata = 0;
|
||||
restartinfo = 0;
|
||||
one_coeff = 1;
|
||||
|
|
@ -46,7 +46,7 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
|||
py_potential = NULL;
|
||||
|
||||
// add current directory to PYTHONPATH
|
||||
PyObject * py_path = PySys_GetObject("path");
|
||||
PyObject * py_path = PySys_GetObject((char *)"path");
|
||||
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
|
||||
|
||||
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
|
||||
|
|
@ -353,3 +353,83 @@ double PairPython::init_one(int, int)
|
|||
return cut_global;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairPython::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
|
||||
// prepare access to compute_force and compute_energy functions
|
||||
|
||||
PyGILState_STATE gstate = PyGILState_Ensure();
|
||||
PyObject *py_pair_instance = (PyObject *) py_potential;
|
||||
PyObject *py_compute_force
|
||||
= PyObject_GetAttrString(py_pair_instance,"compute_force");
|
||||
if (!py_compute_force) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_force' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_force)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_force' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_compute_energy
|
||||
= PyObject_GetAttrString(py_pair_instance,"compute_energy");
|
||||
if (!py_compute_energy) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not find 'compute_energy' method'");
|
||||
}
|
||||
if (!PyCallable_Check(py_compute_energy)) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Python 'compute_energy' is not callable");
|
||||
}
|
||||
|
||||
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
|
||||
PyObject *py_compute_args = PyTuple_New(3);
|
||||
if (!py_compute_args) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
|
||||
}
|
||||
|
||||
py_itype = PY_INT_FROM_LONG(itype);
|
||||
PyTuple_SetItem(py_compute_args,1,py_itype);
|
||||
py_jtype = PY_INT_FROM_LONG(jtype);
|
||||
PyTuple_SetItem(py_compute_args,2,py_jtype);
|
||||
py_rsq = PyFloat_FromDouble(rsq);
|
||||
PyTuple_SetItem(py_compute_args,0,py_rsq);
|
||||
|
||||
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'compute_force' function failed");
|
||||
}
|
||||
fforce = factor_lj*PyFloat_AsDouble(py_value)/rsq;
|
||||
|
||||
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
|
||||
if (!py_value) {
|
||||
PyErr_Print();
|
||||
PyErr_Clear();
|
||||
PyGILState_Release(gstate);
|
||||
error->all(FLERR,"Calling 'compute_energy' function failed");
|
||||
}
|
||||
double evdwl = factor_lj*PyFloat_AsDouble(py_value);
|
||||
|
||||
Py_DECREF(py_compute_args);
|
||||
PyGILState_Release(gstate);
|
||||
|
||||
return evdwl;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -42,6 +42,7 @@ class PairPython : public Pair {
|
|||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
|
|
|||
Loading…
Reference in New Issue