adding Pair::single() support to python pair style and examples (43efe9e4) · Commits · 郑智淋 / lammps

examples/python/data.spce

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examples/python/in.pair_python_coulomb

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Original line number	Diff line number	Diff line
		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

examples/python/in.pair_python_table

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Original line number	Diff line number	Diff line
		# 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

examples/python/log.4May17.pair_python_coulomb.1

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Original line number	Diff line number	Diff line
		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

examples/python/log.4May17.pair_python_coulomb.4

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Original line number	Diff line number	Diff line
		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

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