provide reference output for python pair style inputs (6a1f7e61) · Commits · 郑智淋 / lammps

examples/python/log.4May2017.pair_python_hybrid.g++.1

0 → 100644

+250 −0

Original line number	Diff line number	Diff line
		LAMMPS (4 May 2017)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		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)
		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 hybrid lj/cut 2.5 python 2.5
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 4.828 \| 4.828 \| 4.828 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 3 -6.7733681 0 -2.2744931 -3.7033504
		50 1.6758903 -4.7955425 0 -2.2823355 5.670064
		100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
		150 1.6324555 -4.7286791 0 -2.280608 5.9589514
		200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
		250 1.6275257 -4.7224992 0 -2.281821 5.9567365
		Loop time of 41.3888 on 1 procs for 250 steps with 4000 atoms

		Performance: 2609.399 tau/day, 6.040 timesteps/s
		48.7% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 41.135 \| 41.135 \| 41.135 \| 0.0 \| 99.39
		Neigh \| 0.17089 \| 0.17089 \| 0.17089 \| 0.0 \| 0.41
		Comm \| 0.032175 \| 0.032175 \| 0.032175 \| 0.0 \| 0.08
		Output \| 0.000513 \| 0.000513 \| 0.000513 \| 0.0 \| 0.00
		Modify \| 0.046448 \| 0.046448 \| 0.046448 \| 0.0 \| 0.11
		Other \| \| 0.003913 \| \| \| 0.01

		Nlocal: 4000 ave 4000 max 4000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 5499 ave 5499 max 5499 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		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
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task

		read_restart hybrid.restart
		orthogonal box = (0 0 0) to (16.796 16.796 16.796)
		1 by 1 by 1 MPI processor grid
		4000 atoms

		pair_style hybrid lj/cut 2.5 python 2.5
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 4.626 \| 4.626 \| 4.626 Mbytes
		Step Temp E_pair E_mol TotEng Press
		250 1.6275257 -4.7224992 0 -2.281821 5.9567365
		300 1.645592 -4.7496711 0 -2.2819002 5.8734193
		350 1.6514972 -4.7580756 0 -2.2814491 5.810167
		400 1.6540555 -4.7622999 0 -2.281837 5.8200413
		450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
		500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
		Loop time of 41.5677 on 1 procs for 250 steps with 4000 atoms

		Performance: 2598.172 tau/day, 6.014 timesteps/s
		48.7% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 41.124 \| 41.124 \| 41.124 \| 0.0 \| 98.93
		Neigh \| 0.35605 \| 0.35605 \| 0.35605 \| 0.0 \| 0.86
		Comm \| 0.034799 \| 0.034799 \| 0.034799 \| 0.0 \| 0.08
		Output \| 0.000473 \| 0.000473 \| 0.000473 \| 0.0 \| 0.00
		Modify \| 0.046841 \| 0.046841 \| 0.046841 \| 0.0 \| 0.11
		Other \| \| 0.005854 \| \| \| 0.01

		Nlocal: 4000 ave 4000 max 4000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 5472 ave 5472 max 5472 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 0
		Ave neighs/atom = 0
		Neighbor list builds = 25
		Dangerous builds = 25

		clear
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		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)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		4000 atoms
		reading velocities ...
		4000 velocities

		pair_style hybrid lj/cut 2.5 python 2.5
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 4.126 \| 4.126 \| 4.126 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 1.6275257 -4.7224992 0 -2.281821 5.9567365
		50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
		100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
		150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
		200 1.6258731 -4.7205017 0 -2.2823017 5.952511
		250 1.6370862 -4.7373176 0 -2.2823022 5.925807
		Loop time of 41.7098 on 1 procs for 250 steps with 4000 atoms

		Performance: 2589.318 tau/day, 5.994 timesteps/s
		48.7% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 41.458 \| 41.458 \| 41.458 \| 0.0 \| 99.40
		Neigh \| 0.16992 \| 0.16992 \| 0.16992 \| 0.0 \| 0.41
		Comm \| 0.031355 \| 0.031355 \| 0.031355 \| 0.0 \| 0.08
		Output \| 0.000537 \| 0.000537 \| 0.000537 \| 0.0 \| 0.00
		Modify \| 0.046569 \| 0.046569 \| 0.046569 \| 0.0 \| 0.11
		Other \| \| 0.003735 \| \| \| 0.01

		Nlocal: 4000 ave 4000 max 4000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 5487 ave 5487 max 5487 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 0
		Ave neighs/atom = 0
		Neighbor list builds = 12
		Dangerous builds not checked

		shell rm hybrid.data hybrid.restart
		Total wall time: 0:02:07

examples/python/log.4May2017.pair_python_hybrid.g++.4

0 → 100644

+250 −0

Original line number	Diff line number	Diff line
		LAMMPS (4 May 2017)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		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)
		1 by 1 by 2 MPI processor grid
		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
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 4.044 \| 4.044 \| 4.044 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 3 -6.7733681 0 -2.2744931 -3.7033504
		50 1.6758903 -4.7955425 0 -2.2823355 5.670064
		100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
		150 1.6324555 -4.7286791 0 -2.280608 5.9589514
		200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
		250 1.6275257 -4.7224992 0 -2.281821 5.9567365
		Loop time of 33.3499 on 2 procs for 250 steps with 4000 atoms

		Performance: 3238.386 tau/day, 7.496 timesteps/s
		31.8% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 31.739 \| 32.45 \| 33.16 \| 12.5 \| 97.30
		Neigh \| 0.12882 \| 0.1292 \| 0.12959 \| 0.1 \| 0.39
		Comm \| 0.04094 \| 0.75173 \| 1.4625 \| 82.0 \| 2.25
		Output \| 0.000352 \| 0.0004115 \| 0.000471 \| 0.0 \| 0.00
		Modify \| 0.014923 \| 0.01509 \| 0.015257 \| 0.1 \| 0.05
		Other \| \| 0.003902 \| \| \| 0.01

		Nlocal: 2000 ave 2006 max 1994 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 3942 ave 3967 max 3917 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 0 ave 0 max 0 min
		Histogram: 2 0 0 0 0 0 0 0 0 0

		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
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task

		read_restart hybrid.restart
		orthogonal box = (0 0 0) to (16.796 16.796 16.796)
		1 by 1 by 2 MPI processor grid
		4000 atoms

		pair_style hybrid lj/cut 2.5 python 2.5
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 3.747 \| 3.747 \| 3.747 Mbytes
		Step Temp E_pair E_mol TotEng Press
		250 1.6275257 -4.7224992 0 -2.281821 5.9567365
		300 1.645592 -4.7496711 0 -2.2819002 5.8734193
		350 1.6514972 -4.7580756 0 -2.2814491 5.810167
		400 1.6540555 -4.7622999 0 -2.281837 5.8200413
		450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
		500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
		Loop time of 33.4436 on 2 procs for 250 steps with 4000 atoms

		Performance: 3229.315 tau/day, 7.475 timesteps/s
		31.8% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 31.79 \| 32.446 \| 33.101 \| 11.5 \| 97.02
		Neigh \| 0.26891 \| 0.26902 \| 0.26912 \| 0.0 \| 0.80
		Comm \| 0.051997 \| 0.70764 \| 1.3633 \| 77.9 \| 2.12
		Output \| 0.000332 \| 0.000396 \| 0.00046 \| 0.0 \| 0.00
		Modify \| 0.01539 \| 0.015553 \| 0.015717 \| 0.1 \| 0.05
		Other \| \| 0.005483 \| \| \| 0.02

		Nlocal: 2000 ave 2000 max 2000 min
		Histogram: 2 0 0 0 0 0 0 0 0 0
		Nghost: 3912 ave 3920 max 3904 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 0 ave 0 max 0 min
		Histogram: 2 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 0
		Ave neighs/atom = 0
		Neighbor list builds = 25
		Dangerous builds = 25

		clear
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		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)
		1 by 1 by 2 MPI processor grid
		reading atoms ...
		4000 atoms
		reading velocities ...
		4000 velocities

		pair_style hybrid lj/cut 2.5 python 2.5
		pair_coeff * * python lj-melt-potential.py lj NULL
		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
		Per MPI rank memory allocation (min/avg/max) = 3.247 \| 3.247 \| 3.247 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 1.6275257 -4.7224992 0 -2.281821 5.9567365
		50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
		100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
		150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
		200 1.6258731 -4.7205017 0 -2.2823017 5.952511
		250 1.6370862 -4.7373176 0 -2.2823022 5.925807
		Loop time of 33.0043 on 2 procs for 250 steps with 4000 atoms

		Performance: 3272.302 tau/day, 7.575 timesteps/s
		31.8% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 31.676 \| 32.248 \| 32.819 \| 10.1 \| 97.71
		Neigh \| 0.12725 \| 0.12751 \| 0.12778 \| 0.1 \| 0.39
		Comm \| 0.038764 \| 0.60973 \| 1.1807 \| 73.1 \| 1.85
		Output \| 0.000359 \| 0.000424 \| 0.000489 \| 0.0 \| 0.00
		Modify \| 0.015441 \| 0.01555 \| 0.01566 \| 0.1 \| 0.05
		Other \| \| 0.003519 \| \| \| 0.01

		Nlocal: 2000 ave 2004 max 1996 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 3923.5 ave 3927 max 3920 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 0 ave 0 max 0 min
		Histogram: 2 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 0
		Ave neighs/atom = 0
		Neighbor list builds = 12
		Dangerous builds not checked

		shell rm hybrid.data hybrid.restart
		Total wall time: 0:01:42

examples/python/log.4May2017.pair_python_melt.g++.1

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examples/python/log.4May2017.pair_python_melt.g++.4

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