add lj example for fix widom (c9342aec) · Commits · 郑智淋 / lammps

examples/gcmc/data.widom.lj

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examples/gcmc/in.widom.lj

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		# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)

		units lj
		atom_style atomic

		pair_style lj/cut 2.5
		pair_modify shift yes

		read_data data.widom.lj

		pair_coeff 1 1 1.0 1.0 2.5
		pair_coeff 1 2 1.5 0.8 2.0
		pair_coeff 2 2 0.5 0.88 2.2

		neighbor 0.3 bin
		neigh_modify delay 0 every 5 check yes

		fix mywidom all widom 10 100000 2 29494 0.75

		fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
		fix 2 all nve

		timestep 0.002

		thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
		thermo 10

		run 100

examples/gcmc/log.30Jun20.widom.lj.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (30 Jun 2020)
		using 1 OpenMP thread(s) per MPI task
		# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)

		units lj
		atom_style atomic

		pair_style lj/cut 2.5
		pair_modify shift yes

		read_data data.widom.lj
		orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		1000 atoms
		reading velocities ...
		1000 velocities
		read_data CPU = 0.003 seconds

		pair_coeff 1 1 1.0 1.0 2.5
		pair_coeff 1 2 1.5 0.8 2.0
		pair_coeff 2 2 0.5 0.88 2.2

		neighbor 0.3 bin
		neigh_modify delay 0 every 5 check yes

		fix mywidom all widom 10 100000 2 29494 0.75

		fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
		fix 2 all nve

		timestep 0.002

		thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
		thermo 10

		run 100
		Neighbor list info ...
		update every 5 steps, delay 0 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 = 7 7 7
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut, 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) = 3.181 \| 3.181 \| 3.181 Mbytes
		Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
		0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
		10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
		20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
		30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
		40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
		50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
		60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
		70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
		80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
		90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
		100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
		Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms

		Performance: 669.082 tau/day, 3.872 timesteps/s
		99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.08186 \| 0.08186 \| 0.08186 \| 0.0 \| 0.32
		Neigh \| 0.023613 \| 0.023613 \| 0.023613 \| 0.0 \| 0.09
		Comm \| 0.0053532 \| 0.0053532 \| 0.0053532 \| 0.0 \| 0.02
		Output \| 0.00037837 \| 0.00037837 \| 0.00037837 \| 0.0 \| 0.00
		Modify \| 25.715 \| 25.715 \| 25.715 \| 0.0 \| 99.57
		Other \| \| 0.0005643 \| \| \| 0.00

		Nlocal: 1000.00 ave 1000 max 1000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 3049.00 ave 3049 max 3049 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 46176.0 ave 46176 max 46176 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 46176
		Ave neighs/atom = 46.176000
		Neighbor list builds = 10
		Dangerous builds = 0
		Total wall time: 0:00:25

examples/gcmc/log.30Jun20.widom.lj.g++.4

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Original line number	Diff line number	Diff line
		LAMMPS (30 Jun 2020)
		using 1 OpenMP thread(s) per MPI task
		# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)

		units lj
		atom_style atomic

		pair_style lj/cut 2.5
		pair_modify shift yes

		read_data data.widom.lj
		orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		1000 atoms
		reading velocities ...
		1000 velocities
		read_data CPU = 0.002 seconds

		pair_coeff 1 1 1.0 1.0 2.5
		pair_coeff 1 2 1.5 0.8 2.0
		pair_coeff 2 2 0.5 0.88 2.2

		neighbor 0.3 bin
		neigh_modify delay 0 every 5 check yes

		fix mywidom all widom 10 100000 2 29494 0.75

		fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
		fix 2 all nve

		timestep 0.002

		thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
		thermo 10

		run 100
		Neighbor list info ...
		update every 5 steps, delay 0 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 = 7 7 7
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut, 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) = 3.13 \| 3.13 \| 3.131 Mbytes
		Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
		0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
		10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
		20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
		30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
		40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
		50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
		60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
		70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
		80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
		90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
		100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
		Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms

		Performance: 5116.239 tau/day, 29.608 timesteps/s
		98.7% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.02025 \| 0.020952 \| 0.021322 \| 0.3 \| 0.62
		Neigh \| 0.0059071 \| 0.0060568 \| 0.0061543 \| 0.1 \| 0.18
		Comm \| 0.016558 \| 0.059554 \| 0.094282 \| 12.2 \| 1.76
		Output \| 0.00022173 \| 0.00042927 \| 0.0010471 \| 0.0 \| 0.01
		Modify \| 3.2552 \| 3.2902 \| 3.3335 \| 1.7 \| 97.42
		Other \| \| 0.0003003 \| \| \| 0.01

		Nlocal: 250.000 ave 256 max 242 min
		Histogram: 1 0 0 0 1 0 0 0 1 1
		Nghost: 1666.00 ave 1670 max 1659 min
		Histogram: 1 0 0 0 0 0 1 0 0 2
		Neighs: 11538.0 ave 11832 max 11091 min
		Histogram: 1 0 0 0 0 0 1 1 0 1

		Total # of neighbors = 46152
		Ave neighs/atom = 46.152000
		Neighbor list builds = 10
		Dangerous builds = 0
		Total wall time: 0:00:03

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