add polyethylene airebo example for future reference (fa469ae1) · Commits · 郑智淋 / lammps

examples/airebo/data.airebo

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Original line number	Diff line number	Diff line
		LAMMPS data file from restart file: timestep = 1, procs = 1

		60 atoms

		2 atom types

		-2.1 2.1 xlo xhi
		-2.1 2.1 ylo yhi
		0 25.5790000000 zlo zhi

		Masses

		1 12.01
		2 1.00794

		Atoms

		1 1 0.0000000000 0.0000000000 0.0000000000
		2 2 0.9010066786 -0.6310205743 0.0000000000
		3 2 -0.9010066786 -0.6310205743 0.0000000000
		4 1 0.0000000000 0.8470061967 1.2789591482
		5 2 0.9010066786 1.4780267710 1.2789591482
		6 2 -0.9010066786 1.4780267710 1.2789591482
		7 1 0.0000000000 0.0000000000 2.5579182965
		8 2 0.9010066786 -0.6310205743 2.5579182965
		9 2 -0.9010066786 -0.6310205743 2.5579182965
		10 1 0.0000000000 0.8470061967 3.8368774447
		11 2 0.9010066786 1.4780267710 3.8368774447
		12 2 -0.9010066786 1.4780267710 3.8368774447
		13 1 0.0000000000 0.0000000000 5.1158365929
		14 2 0.9010066786 -0.6310205743 5.1158365929
		15 2 -0.9010066786 -0.6310205743 5.1158365929
		16 1 0.0000000000 0.8470061967 6.3947957411
		17 2 0.9010066786 1.4780267710 6.3947957411
		18 2 -0.9010066786 1.4780267710 6.3947957411
		19 1 0.0000000000 0.0000000000 7.6737548894
		20 2 0.9010066786 -0.6310205743 7.6737548894
		21 2 -0.9010066786 -0.6310205743 7.6737548894
		22 1 0.0000000000 0.8470061967 8.9527140376
		23 2 0.9010066786 1.4780267710 8.9527140376
		24 2 -0.9010066786 1.4780267710 8.9527140376
		25 1 0.0000000000 0.0000000000 10.2316731858
		26 2 0.9010066786 -0.6310205743 10.2316731858
		27 2 -0.9010066786 -0.6310205743 10.2316731858
		28 1 0.0000000000 0.8470061967 11.5106323340
		29 2 0.9010066786 1.4780267710 11.5106323340
		30 2 -0.9010066786 1.4780267710 11.5106323340
		31 1 0.0000000000 0.0000000000 12.7895914823
		32 2 0.9010066786 -0.6310205743 12.7895914823
		33 2 -0.9010066786 -0.6310205743 12.7895914823
		34 1 0.0000000000 0.8470061967 14.0685506305
		35 2 0.9010066786 1.4780267710 14.0685506305
		36 2 -0.9010066786 1.4780267710 14.0685506305
		37 1 0.0000000000 0.0000000000 15.3475097787
		38 2 0.9010066786 -0.6310205743 15.3475097787
		39 2 -0.9010066786 -0.6310205743 15.3475097787
		40 1 0.0000000000 0.8470061967 16.6264689269
		41 2 0.9010066786 1.4780267710 16.6264689269
		42 2 -0.9010066786 1.4780267710 16.6264689269
		43 1 0.0000000000 0.0000000000 17.9054280752
		44 2 0.9010066786 -0.6310205743 17.9054280752
		45 2 -0.9010066786 -0.6310205743 17.9054280752
		46 1 0.0000000000 0.8470061967 19.1843872234
		47 2 0.9010066786 1.4780267710 19.1843872234
		48 2 -0.9010066786 1.4780267710 19.1843872234
		49 1 0.0000000000 0.0000000000 20.4633463716
		50 2 0.9010066786 -0.6310205743 20.4633463716
		51 2 -0.9010066786 -0.6310205743 20.4633463716
		52 1 0.0000000000 0.8470061967 21.7423055198
		53 2 0.9010066786 1.4780267710 21.7423055198
		54 2 -0.9010066786 1.4780267710 21.7423055198
		55 1 0.0000000000 0.0000000000 23.0212646681
		56 2 0.9010066786 -0.6310205743 23.0212646681
		57 2 -0.9010066786 -0.6310205743 23.0212646681
		58 1 0.0000000000 0.8470061967 24.3002238163
		59 2 0.9010066786 1.4780267710 24.3002238163
		60 2 -0.9010066786 1.4780267710 24.3002238163

examples/airebo/in.airebo

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Original line number	Diff line number	Diff line
		# AIREBO polyethelene benchmark

		units metal
		atom_style atomic

		read_data data.airebo

		replicate 17 16 2

		neighbor 0.5 bin
		neigh_modify delay 5 every 1

		pair_style airebo 3.0 1 1
		pair_coeff * * ../../potentials/CH.airebo C H

		velocity all create 300.0 761341

		fix 1 all nve
		timestep 0.0005

		thermo 10
		run 100

examples/airebo/in.airebo-m

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+22 −0

Original line number	Diff line number	Diff line
		# AIREBO polyethelene benchmark

		units metal
		atom_style atomic

		read_data data.airebo

		replicate 17 16 2

		neighbor 0.5 bin
		neigh_modify delay 5 every 1

		pair_style airebo/morse 3.0 1 1
		pair_coeff * * ../../potentials/CH.airebo-m C H

		velocity all create 300.0 761341

		fix 1 all nve
		timestep 0.0005

		thermo 10
		run 100

examples/airebo/log.23Jun17.airebo-m.g++.1

0 → 100644

+86 −0

Original line number	Diff line number	Diff line
		LAMMPS (23 Jun 2017)
		using 1 OpenMP thread(s) per MPI task
		# AIREBO polyethelene benchmark

		units metal
		atom_style atomic

		read_data data.airebo
		orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		60 atoms

		replicate 17 16 2
		orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
		1 by 1 by 1 MPI processor grid
		32640 atoms

		neighbor 0.5 bin
		neigh_modify delay 5 every 1

		pair_style airebo/morse 3.0 1 1
		pair_coeff * * ../../potentials/CH.airebo-m C H
		Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15

		velocity all create 300.0 761341

		fix 1 all nve
		timestep 0.0005

		thermo 10
		run 100
		Neighbor list info ...
		update every 1 steps, delay 5 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 10.7
		ghost atom cutoff = 10.7
		binsize = 5.35, bins = 14 13 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair airebo/morse, perpetual
		attributes: full, newton on, ghost
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 106.4 \| 106.4 \| 106.4 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 300 -139283.82 0 -138018.14 152.25271
		10 166.76148 -138718.75 0 -138015.19 17412.343
		20 207.7293 -138891.79 0 -138015.4 -19395.339
		30 138.54469 -138596.42 0 -138011.92 -11909.248
		40 153.95239 -138661.7 0 -138012.19 -2448.7701
		50 126.22907 -138545.12 0 -138012.57 5206.1374
		60 181.02757 -138778.28 0 -138014.54 22506.777
		70 185.72779 -138799.18 0 -138015.61 -10803.744
		80 164.28396 -138709.5 0 -138016.4 -1524.7353
		90 180.26403 -138776.42 0 -138015.9 -27143.467
		100 164.05694 -138706.58 0 -138014.44 5157.5516
		Loop time of 117.672 on 1 procs for 100 steps with 32640 atoms

		Performance: 0.037 ns/day, 653.734 hours/ns, 0.850 timesteps/s
		99.3% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 108.31 \| 108.31 \| 108.31 \| 0.0 \| 92.04
		Neigh \| 9.2199 \| 9.2199 \| 9.2199 \| 0.0 \| 7.84
		Comm \| 0.052942 \| 0.052942 \| 0.052942 \| 0.0 \| 0.04
		Output \| 0.0015149 \| 0.0015149 \| 0.0015149 \| 0.0 \| 0.00
		Modify \| 0.060962 \| 0.060962 \| 0.060962 \| 0.0 \| 0.05
		Other \| \| 0.02656 \| \| \| 0.02

		Nlocal: 32640 ave 32640 max 32640 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 48094 ave 48094 max 48094 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
		FullNghs: 2.22109e+07 ave 2.22109e+07 max 2.22109e+07 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 22210922
		Ave neighs/atom = 680.482
		Neighbor list builds = 8
		Dangerous builds = 0
		Total wall time: 0:02:00

examples/airebo/log.23Jun17.airebo-m.g++.4

0 → 100644

+86 −0

Original line number	Diff line number	Diff line
		LAMMPS (23 Jun 2017)
		using 1 OpenMP thread(s) per MPI task
		# AIREBO polyethelene benchmark

		units metal
		atom_style atomic

		read_data data.airebo
		orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
		1 by 1 by 4 MPI processor grid
		reading atoms ...
		60 atoms

		replicate 17 16 2
		orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
		2 by 2 by 1 MPI processor grid
		32640 atoms

		neighbor 0.5 bin
		neigh_modify delay 5 every 1

		pair_style airebo/morse 3.0 1 1
		pair_coeff * * ../../potentials/CH.airebo-m C H
		Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15

		velocity all create 300.0 761341

		fix 1 all nve
		timestep 0.0005

		thermo 10
		run 100
		Neighbor list info ...
		update every 1 steps, delay 5 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 10.7
		ghost atom cutoff = 10.7
		binsize = 5.35, bins = 14 13 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair airebo/morse, perpetual
		attributes: full, newton on, ghost
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 29.37 \| 29.75 \| 30.13 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 300 -139283.82 0 -138018.14 152.25271
		10 166.76148 -138718.75 0 -138015.19 17412.343
		20 207.7293 -138891.79 0 -138015.4 -19395.339
		30 138.54469 -138596.42 0 -138011.92 -11909.248
		40 153.95239 -138661.7 0 -138012.19 -2448.7701
		50 126.22907 -138545.12 0 -138012.57 5206.1374
		60 181.02757 -138778.28 0 -138014.54 22506.777
		70 185.72779 -138799.18 0 -138015.61 -10803.744
		80 164.28396 -138709.5 0 -138016.4 -1524.7353
		90 180.26403 -138776.42 0 -138015.9 -27143.467
		100 164.05694 -138706.58 0 -138014.44 5157.5516
		Loop time of 32.9268 on 4 procs for 100 steps with 32640 atoms

		Performance: 0.131 ns/day, 182.927 hours/ns, 3.037 timesteps/s
		99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 28.045 \| 28.537 \| 29.42 \| 10.4 \| 86.67
		Neigh \| 3.163 \| 3.237 \| 3.3761 \| 4.7 \| 9.83
		Comm \| 0.09883 \| 1.1206 \| 1.6862 \| 60.4 \| 3.40
		Output \| 0.00099325 \| 0.0011329 \| 0.0012462 \| 0.3 \| 0.00
		Modify \| 0.016013 \| 0.016726 \| 0.017257 \| 0.4 \| 0.05
		Other \| \| 0.01459 \| \| \| 0.04

		Nlocal: 8160 ave 8167 max 8153 min
		Histogram: 1 0 1 0 0 0 0 1 0 1
		Nghost: 22581 ave 22594 max 22569 min
		Histogram: 1 0 0 0 1 1 0 0 0 1
		Neighs: 0 ave 0 max 0 min
		Histogram: 4 0 0 0 0 0 0 0 0 0
		FullNghs: 5.55273e+06 ave 5.55908e+06 max 5.54496e+06 min
		Histogram: 1 0 0 0 0 1 1 0 0 1

		Total # of neighbors = 22210922
		Ave neighs/atom = 680.482
		Neighbor list builds = 8
		Dangerous builds = 0
		Total wall time: 0:00:33

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