add example input for compute cnp/atom (2b3c124e) · Commits · 郑智淋 / lammps

examples/USER/misc/cnp/Cu_Mishin1.eam

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examples/USER/misc/cnp/in.cnp

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Original line number	Diff line number	Diff line
		# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal

		# Initialization
		units metal
		boundary p p p
		atom_style atomic

		# create simulation box and system
		lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0
		region mdbox block 0 3 0.0 14.0 0 84 units lattice
		region system block 0 3 1.1 13.1 0 84 units lattice
		create_box 2 mdbox
		create_atoms 1 region system

		# Define atoms mass and force field
		mass * 63.54
		pair_style eam/alloy
		pair_coeff * * Cu_Mishin1.eam Cu Cu

		# Delete a plane of atoms along the z direction to generate a partial dislocation
		region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
		delete_atoms region dislocation_atoms
		region quarter_up block 0 3 7 11 0 84 units lattice
		group middle region quarter_up

		# specify simulation parameters
		timestep 0.004

		# Relax configuration using conjugate gradient
		#min_style cg
		#minimize 1.0e-4 1.0e-6 100 1000

		# Setup calculations
		compute 1 all cnp/atom 3.086
		compute 2 all cna/atom 3.086
		compute 3 all centro/atom fcc
		compute 4 all coord/atom cutoff 3.086
		dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4

		### Set up thermo display
		thermo 10
		thermo_style custom step atoms temp press pe ke etotal

		# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
		fix 1 all nve
		fix 2 all langevin 50 1 0.1 699483
		fix 3 all setforce NULL 0.0 NULL
		fix 4 middle setforce 0.0 0.0 0.0
		run 100
		unfix 4
		run 200

examples/USER/misc/cnp/log.31May17.cnp.g++.4

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Original line number	Diff line number	Diff line
		LAMMPS (19 May 2017)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task
		# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal

		# Initialization
		units metal
		boundary p p p
		atom_style atomic

		# create simulation box and system
		lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0
		Lattice spacing in x,y,z = 5.90327 6.26136 5.11238
		region mdbox block 0 3 0.0 14.0 0 84 units lattice
		region system block 0 3 1.1 13.1 0 84 units lattice
		create_box 2 mdbox
		Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44)
		1 by 1 by 4 MPI processor grid
		create_atoms 1 region system
		Created 48384 atoms

		# Define atoms mass and force field
		mass * 63.54
		pair_style eam/alloy
		pair_coeff * * Cu_Mishin1.eam Cu Cu

		# Delete a plane of atoms along the z direction to generate a partial dislocation
		region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
		delete_atoms region dislocation_atoms
		Deleted 76 atoms, new total = 48308
		region quarter_up block 0 3 7 11 0 84 units lattice
		group middle region quarter_up
		16080 atoms in group middle

		# specify simulation parameters
		timestep 0.004

		# Relax configuration using conjugate gradient
		#min_style cg
		#minimize 1.0e-4 1.0e-6 100 1000

		# Setup calculations
		compute 1 all cnp/atom 3.086
		compute 2 all cna/atom 3.086
		compute 3 all centro/atom fcc
		compute 4 all coord/atom cutoff 3.086
		dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4

		### Set up thermo display
		thermo 10
		thermo_style custom step atoms temp press pe ke etotal

		# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
		fix 1 all nve
		fix 2 all langevin 50 1 0.1 699483
		fix 3 all setforce NULL 0.0 NULL
		fix 4 middle setforce 0.0 0.0 0.0
		run 100
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 7.50679
		ghost atom cutoff = 7.50679
		binsize = 3.75339, bins = 5 24 115
		5 neighbor lists, perpetual/occasional/extra = 1 4 0
		(1) pair eam/alloy, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) compute cnp/atom, occasional
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		(3) compute cna/atom, occasional
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		(4) compute centro/atom, occasional
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		(5) compute coord/atom, occasional
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 45.41 \| 45.41 \| 45.41 Mbytes
		Step Atoms Temp Press PotEng KinEng TotEng
		0 48308 0 -3388.0911 -169746.07 0 -169746.07
		10 48308 7.35092 -3091.0864 -169715.96 45.900393 -169670.05
		20 48308 9.9162268 -2822.7045 -169678.51 61.918604 -169616.59
		30 48308 12.351316 -2726.7195 -169666.35 77.123716 -169589.23
		40 48308 13.302856 -2703.586 -169662.9 83.06529 -169579.83
		50 48308 12.782228 -2706.8662 -169662.36 79.814401 -169582.55
		60 48308 12.198179 -2772.4206 -169670.02 76.167503 -169593.86
		70 48308 10.663322 -2841.3384 -169677.48 66.583595 -169610.9
		80 48308 9.1169804 -2932.3896 -169687.85 56.927974 -169630.92
		90 48308 7.2905076 -3029.9433 -169699.09 45.523167 -169653.56
		100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89
		Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms

		Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s
		31.8% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 9.8764 \| 9.9587 \| 10.021 \| 1.6 \| 91.36
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.1232 \| 0.18385 \| 0.26683 \| 12.1 \| 1.69
		Output \| 0.45385 \| 0.45451 \| 0.45634 \| 0.2 \| 4.17
		Modify \| 0.25026 \| 0.2537 \| 0.25744 \| 0.5 \| 2.33
		Other \| \| 0.04949 \| \| \| 0.45

		Nlocal: 12077 ave 12096 max 12020 min
		Histogram: 1 0 0 0 0 0 0 0 0 3
		Nghost: 14204 ave 14261 max 14109 min
		Histogram: 1 0 0 0 0 1 0 0 0 2
		Neighs: 814050 ave 818584 max 809212 min
		Histogram: 1 0 0 0 0 2 0 0 0 1
		FullNghs: 1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min
		Histogram: 1 0 0 0 0 0 1 0 0 2

		Total # of neighbors = 6512400
		Ave neighs/atom = 134.81
		Neighbor list builds = 0
		Dangerous builds = 0
		unfix 4
		run 200
		Per MPI rank memory allocation (min/avg/max) = 45.41 \| 45.41 \| 45.41 Mbytes
		Step Atoms Temp Press PotEng KinEng TotEng
		100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89
		110 48308 15.260795 -2793.119 -169677.24 95.290993 -169581.95
		120 48308 18.548656 -2433.1584 -169624.79 115.82096 -169508.97
		130 48308 22.15831 -2276.626 -169604.28 138.36025 -169465.92
		140 48308 24.393841 -2208.1771 -169596.16 152.31929 -169443.84
		150 48308 24.797558 -2173.3145 -169591.43 154.84016 -169436.59
		160 48308 24.73371 -2188.909 -169593.08 154.44148 -169438.64
		170 48308 24.128467 -2220.3404 -169596.96 150.66225 -169446.29
		180 48308 22.975708 -2275.1244 -169602.72 143.46422 -169459.26
		190 48308 21.936324 -2348.3762 -169610.59 136.97413 -169473.61
		200 48308 20.516249 -2432.8447 -169619.98 128.10694 -169491.87
		210 48308 19.000566 -2510.2915 -169628.58 118.64276 -169509.93
		220 48308 17.490407 -2597.299 -169638.24 109.21307 -169529.03
		230 48308 16.062482 -2684.1203 -169648.31 100.29687 -169548.01
		240 48308 14.360342 -2768.2313 -169657.7 89.668411 -169568.03
		250 48308 12.802315 -2852.6965 -169666.99 79.939831 -169587.05
		260 48308 11.258205 -2944.4533 -169677.52 70.298142 -169607.23
		270 48308 9.6159129 -3038.6304 -169688.06 60.043393 -169628.02
		280 48308 7.972425 -3129.0826 -169698.03 49.781176 -169648.25
		290 48308 6.3752377 -3219.2054 -169708.23 39.808067 -169668.42
		300 48308 4.7374688 -3306.1468 -169718.27 29.58156 -169688.69
		Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms

		Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s
		31.8% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 20.221 \| 20.423 \| 20.57 \| 3.1 \| 88.73
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.27748 \| 0.42603 \| 0.62832 \| 21.4 \| 1.85
		Output \| 1.5454 \| 1.5473 \| 1.5529 \| 0.3 \| 6.72
		Modify \| 0.48886 \| 0.49773 \| 0.50842 \| 1.1 \| 2.16
		Other \| \| 0.1221 \| \| \| 0.53

		Nlocal: 12077 ave 12096 max 12020 min
		Histogram: 1 0 0 0 0 0 0 0 0 3
		Nghost: 14204 ave 14261 max 14109 min
		Histogram: 1 0 0 0 0 1 0 0 0 2
		Neighs: 814094 ave 818584 max 809212 min
		Histogram: 1 0 0 0 0 2 0 0 0 1
		FullNghs: 1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min
		Histogram: 1 0 0 0 0 0 0 1 0 2

		Total # of neighbors = 6514094
		Ave neighs/atom = 134.845
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:00:35

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