(f95ccaf0) · Commits · 郑智淋 / lammps

examples/colloid/log.colloid.22Jun07.liberty.4

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Original line number	Diff line number	Diff line
		LAMMPS (22 June 2007)
		# Big colloid particles and small LJ particles

		units lj
		atom_style atomic
		dimension 2

		lattice sq 0.01
		Lattice spacing in x,y,z = 10 10 10
		region box block 0 30 0 30 -0.5 0.5
		create_box 2 box
		Created orthogonal box = (0 0 -5) to (300 300 5)
		2 by 2 by 1 processor grid
		create_atoms 1 box
		Created 900 atoms

		set group all type/fraction 2 0.96 23984
		868 settings made for type/fraction

		mass 1 9
		mass 2 1

		velocity all create 1.44 87287 loop geom

		# multi neighbor and comm for efficiency

		neighbor 1 multi
		neigh_modify delay 0
		communicate multi

		# colloid potential

		pair_style colloid 12.5
		pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
		pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
		pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5

		fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
		fix 2 all enforce2d

		dump 1 all atom 200 dump.colloid

		thermo_style custom step temp epair etotal press vol
		thermo 1000

		timestep 0.005

		run 10000
		Memory usage per processor = 1.45054 Mbytes
		Step Temp E_pair TotEng Press Volume
		0 1.44 0 1.4376 0.0009584 900000
		1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331
		2000 1.9719939 0.18486401 2.1535713 0.79205274 4710.4215
		3000 1.8512583 0.19478206 2.0429549 1.2638229 3348.993
		4000 2.0197762 0.085599862 2.1020098 0.44423307 6289.5217
		5000 2.1100188 0.066582351 2.1730844 0.30071147 7797.8952
		6000 2.122322 0.080537323 2.1993221 0.47114461 5829.3235
		7000 2.0053017 0.17924225 2.1812018 0.82372251 4418.5393
		8000 1.9850765 0.16081341 2.1425814 0.86380905 4218.1246
		9000 2.0229633 0.14063325 2.1602249 0.8620141 4223.7169
		10000 2.0133665 0.16380502 2.173816 0.95385436 3995.0006
		Loop time of 4.86636 on 4 procs for 10000 steps with 900 atoms

		Pair time (%) = 1.32706 (27.27)
		Neigh time (%) = 0.274084 (5.63221)
		Comm time (%) = 1.98481 (40.7863)
		Outpt time (%) = 0.0898068 (1.84546)
		Other time (%) = 1.1906 (24.466)

		Nlocal: 225 ave 232 max 218 min
		Histogram: 1 0 0 0 0 2 0 0 0 1
		Nghost: 411.5 ave 428 max 388 min
		Histogram: 1 0 0 0 1 0 0 0 0 2
		Neighs: 2307 ave 2410 max 2183 min
		Histogram: 1 0 1 0 0 0 0 0 0 2

		Total # of neighbors = 9228
		Ave neighs/atom = 10.2533
		Neighbor list builds = 773
		Dangerous builds = 0

examples/colloid/log.colloid.22Jun07.linux.1

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Original line number	Diff line number	Diff line
		LAMMPS (22 June 2007)
		# Big colloid particles and small LJ particles

		units lj
		atom_style atomic
		dimension 2

		lattice sq 0.01
		Lattice spacing in x,y,z = 10 10 10
		region box block 0 30 0 30 -0.5 0.5
		create_box 2 box
		Created orthogonal box = (0 0 -5) to (300 300 5)
		1 by 1 by 1 processor grid
		create_atoms 1 box
		Created 900 atoms

		set group all type/fraction 2 0.96 23984
		868 settings made for type/fraction

		mass 1 9
		mass 2 1

		velocity all create 1.44 87287 loop geom

		# multi neighbor and comm for efficiency

		neighbor 1 multi
		neigh_modify delay 0
		communicate multi

		# colloid potential

		pair_style colloid 12.5
		pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
		pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
		pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5

		fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
		fix 2 all enforce2d

		dump 1 all atom 200 dump.colloid

		thermo_style custom step temp epair etotal press vol
		thermo 1000

		timestep 0.005

		run 10000
		Memory usage per processor = 1.47629 Mbytes
		Step Temp E_pair TotEng Press Volume
		0 1.44 0 1.4376 0.0009584 900000
		1000 1.8470142 0.0048357172 1.8487715 0.017163086 74830.331
		2000 1.9719939 0.18486401 2.1535713 0.79205271 4710.4215
		3000 1.8760117 0.16888745 2.0417724 1.2866805 3349.4362
		4000 2.0084889 0.10591744 2.1110589 0.41080478 6315.195
		5000 2.0845189 0.074837406 2.1558821 0.32123703 7787.3569
		6000 2.0635646 0.12699208 2.1871174 0.55212245 5811.0643
		7000 2.0511741 0.13194486 2.1797003 0.75534937 4447.7483
		8000 2.0057569 0.14524464 2.1476586 0.93321505 4260.455
		9000 1.9863917 0.16294985 2.1460309 0.85687596 4264.0791
		10000 1.9867944 0.17403524 2.1575183 1.019418 3985.5163
		Loop time of 13.1171 on 1 procs for 10000 steps with 900 atoms

		Pair time (%) = 8.49344 (64.7507)
		Neigh time (%) = 1.7079 (13.0204)
		Comm time (%) = 0.409296 (3.12032)
		Outpt time (%) = 0.224203 (1.70924)
		Other time (%) = 2.28229 (17.3993)

		Nlocal: 900 ave 900 max 900 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 648 ave 648 max 648 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 9057 ave 9057 max 9057 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 9057
		Ave neighs/atom = 10.0633
		Neighbor list builds = 777
		Dangerous builds = 0

examples/crack/log.crack.22Jun07.liberty.4

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+129 −0

Original line number	Diff line number	Diff line
		LAMMPS (22 June 2007)
		# 2d LJ crack simulation

		dimension 2
		boundary s s p

		atom_style atomic
		neighbor 0.3 bin
		neigh_modify delay 5

		# create geometry

		lattice hex 0.93
		Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
		region box block 0 100 0 40 -0.25 0.25
		create_box 5 box
		Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
		2 by 2 by 1 processor grid
		create_atoms 1 box
		Created 8141 atoms

		mass 1 1.0
		mass 2 1.0
		mass 3 1.0
		mass 4 1.0
		mass 5 1.0

		# LJ potentials

		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0 2.5

		# define groups

		region 1 block INF INF INF 1.25 INF INF
		group lower region 1
		302 atoms in group lower
		region 2 block INF INF 38.75 INF INF INF
		group upper region 2
		302 atoms in group upper
		group boundary union lower upper
		604 atoms in group boundary
		group mobile subtract all boundary
		7537 atoms in group mobile

		region leftupper block INF 20 20 INF INF INF
		region leftlower block INF 20 INF 20 INF INF
		group leftupper region leftupper
		820 atoms in group leftupper
		group leftlower region leftlower
		841 atoms in group leftlower

		set group leftupper type 2
		820 settings made for type
		set group leftlower type 3
		841 settings made for type
		set group lower type 4
		302 settings made for type
		set group upper type 5
		302 settings made for type

		# initial velocities

		compute new mobile temp
		velocity mobile create 0.01 887723 temp new
		velocity upper set 0.0 0.3 0.0
		velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes

		# fixes

		fix 1 all nve
		fix 2 boundary setforce NULL 0.0 0.0

		# run

		timestep 0.003
		thermo 200
		thermo_modify temp new

		neigh_modify exclude type 2 3
		dump 1 all atom 500 dump.crack
		run 5000
		Memory usage per processor = 1.59725 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.065996472 -3.2595015 0 -3.1984136 -0.04302381 4792.6107
		200 0.060047239 -3.2531973 0 -3.1976162 -0.27194148 4811.0322
		400 0.060540328 -3.2510659 0 -3.1950283 -0.51122765 4832.8487
		600 0.060577107 -3.2468136 0 -3.190742 -0.71796559 4855.0481
		800 0.060812364 -3.241354 0 -3.1850647 -0.89095308 4876.899
		1000 0.061815921 -3.2349951 0 -3.1777768 -1.0418483 4899.229
		1200 0.063180751 -3.227761 0 -3.1692795 -1.1726472 4913.5762
		1400 0.065132588 -3.2198103 0 -3.1595221 -1.279378 4933.6517
		1600 0.067270882 -3.2111519 0 -3.1488844 -1.3695054 4952.9497
		1800 0.0693778 -3.201954 0 -3.1377363 -1.4352657 4975.6762
		2000 0.071252815 -3.1921529 0 -3.1261996 -1.4841334 4994.9699
		2200 0.073149176 -3.181847 0 -3.1141384 -1.5151492 5011.4455
		2400 0.074908709 -3.1710714 0 -3.1017341 -1.5320377 5034.0712
		2600 0.076683014 -3.1599865 0 -3.0890069 -1.5392632 5049.8449
		2800 0.078565789 -3.1486031 0 -3.0758808 -1.5361716 5070.8919
		3000 0.080066913 -3.1368161 0 -3.0627043 -1.5207043 5089.9281
		3200 0.081471767 -3.1247706 0 -3.0493584 -1.4971581 5105.9878
		3400 0.08330546 -3.1128524 0 -3.035743 -1.4631308 5124.3294
		3600 0.08531273 -3.1009259 0 -3.0219584 -1.4242782 5139.7334
		3800 0.086420792 -3.0884931 0 -3.0085 -1.3812881 5151.9744
		4000 0.085220498 -3.0759708 0 -2.9970887 -1.3501547 5163.5493
		4200 0.08235554 -3.0634364 0 -2.9872062 -1.341062 5178.82
		4400 0.08347755 -3.0521602 0 -2.9748914 -1.3473183 5192.4176
		4600 0.084114334 -3.0389835 0 -2.9611253 -1.3384039 5209.5435
		4800 0.085414901 -3.0273902 0 -2.9483282 -1.3365973 5232.9505
		5000 0.087614902 -3.0176386 0 -2.9365402 -1.337001 5251.075
		Loop time of 7.15681 on 4 procs for 5000 steps with 8141 atoms

		Pair time (%) = 4.67775 (65.3608)
		Neigh time (%) = 0.180912 (2.52784)
		Comm time (%) = 1.1892 (16.6164)
		Outpt time (%) = 0.174089 (2.4325)
		Other time (%) = 0.934854 (13.0624)

		Nlocal: 2035.25 ave 2062 max 2008 min
		Histogram: 1 0 0 0 1 1 0 0 0 1
		Nghost: 204.5 ave 246 max 175 min
		Histogram: 2 0 0 0 0 0 1 0 0 1
		Neighs: 17860.5 ave 18270 max 17548 min
		Histogram: 1 0 0 2 0 0 0 0 0 1

		Total # of neighbors = 71442
		Ave neighs/atom = 8.77558
		Neighbor list builds = 98
		Dangerous builds = 0

examples/crack/log.crack.22Jun07.linux.1

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+129 −0

Original line number	Diff line number	Diff line
		LAMMPS (22 June 2007)
		# 2d LJ crack simulation

		dimension 2
		boundary s s p

		atom_style atomic
		neighbor 0.3 bin
		neigh_modify delay 5

		# create geometry

		lattice hex 0.93
		Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
		region box block 0 100 0 40 -0.25 0.25
		create_box 5 box
		Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
		1 by 1 by 1 processor grid
		create_atoms 1 box
		Created 8141 atoms

		mass 1 1.0
		mass 2 1.0
		mass 3 1.0
		mass 4 1.0
		mass 5 1.0

		# LJ potentials

		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0 2.5

		# define groups

		region 1 block INF INF INF 1.25 INF INF
		group lower region 1
		302 atoms in group lower
		region 2 block INF INF 38.75 INF INF INF
		group upper region 2
		302 atoms in group upper
		group boundary union lower upper
		604 atoms in group boundary
		group mobile subtract all boundary
		7537 atoms in group mobile

		region leftupper block INF 20 20 INF INF INF
		region leftlower block INF 20 INF 20 INF INF
		group leftupper region leftupper
		820 atoms in group leftupper
		group leftlower region leftlower
		841 atoms in group leftlower

		set group leftupper type 2
		820 settings made for type
		set group leftlower type 3
		841 settings made for type
		set group lower type 4
		302 settings made for type
		set group upper type 5
		302 settings made for type

		# initial velocities

		compute new mobile temp
		velocity mobile create 0.01 887723 temp new
		velocity upper set 0.0 0.3 0.0
		velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes

		# fixes

		fix 1 all nve
		fix 2 boundary setforce NULL 0.0 0.0

		# run

		timestep 0.003
		thermo 200
		thermo_modify temp new

		neigh_modify exclude type 2 3
		dump 1 all atom 500 dump.crack
		run 5000
		Memory usage per processor = 2.04243 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.065655433 -3.2595015 0 -3.1987293 -0.043381291 4792.6107
		200 0.060090071 -3.2531939 0 -3.1975731 -0.27682436 4811.1142
		400 0.060537254 -3.2509976 0 -3.1949629 -0.51538634 4833.6384
		600 0.060833381 -3.2466952 0 -3.1903864 -0.72165405 4854.5327
		800 0.061681012 -3.2413218 0 -3.1842284 -0.89573177 4876.5182
		1000 0.062387584 -3.2349276 0 -3.1771802 -1.046532 4897.0644
		1200 0.063713197 -3.2276097 0 -3.1686353 -1.1733596 4916.992
		1400 0.065408625 -3.2196611 0 -3.1591173 -1.2802996 4937.9378
		1600 0.067583821 -3.2110381 0 -3.1484809 -1.3713947 4956.9814
		1800 0.069328584 -3.2018539 0 -3.1376817 -1.4389808 4974.9955
		2000 0.071019398 -3.192111 0 -3.1263738 -1.4879518 4992.2457
		2200 0.072997487 -3.1818704 0 -3.1143022 -1.5204135 5014.7654
		2400 0.075005457 -3.1712316 0 -3.1018048 -1.5359222 5031.8024
		2600 0.076848328 -3.1601006 0 -3.088968 -1.5313163 5052.4867
		2800 0.078676694 -3.148775 0 -3.07595 -1.5154187 5070.2113
		3000 0.080718743 -3.137326 0 -3.0626108 -1.4892046 5087.256
		3200 0.083100049 -3.1260245 0 -3.0491051 -1.4538734 5106.4445
		3400 0.085430328 -3.1146626 0 -3.0355863 -1.4172254 5127.5606
		3600 0.087402049 -3.1029496 0 -3.0220482 -1.3687184 5142.5301
		3800 0.089013695 -3.0908222 0 -3.0084291 -1.3168466 5156.5957
		4000 0.089818767 -3.079408 0 -2.9962696 -1.2722766 5169.2872
		4200 0.085852921 -3.0668561 0 -2.9873886 -1.2424995 5184.3213
		4400 0.086203112 -3.0559681 0 -2.9761765 -1.2315726 5195.5481
		4600 0.086772028 -3.0437629 0 -2.9634447 -1.2220387 5213.9452
		4800 0.088200815 -3.0328504 0 -2.9512097 -1.2296115 5232.6714
		5000 0.08942145 -3.0228831 0 -2.9401125 -1.2228214 5255.2593
		Loop time of 45.1427 on 1 procs for 5000 steps with 8141 atoms

		Pair time (%) = 36.1309 (80.0372)
		Neigh time (%) = 1.29244 (2.86301)
		Comm time (%) = 0.075937 (0.168216)
		Outpt time (%) = 0.437291 (0.968687)
		Other time (%) = 7.20605 (15.9628)

		Nlocal: 8141 ave 8141 max 8141 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 71389 ave 71389 max 71389 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 71389
		Ave neighs/atom = 8.76907
		Neighbor list builds = 100
		Dangerous builds = 0

examples/dipole/log.dipole.22Jun07.liberty.4

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+83 −0

Original line number	Diff line number	Diff line
		LAMMPS (22 June 2007)
		# Point dipoles in a 2d box

		units lj
		atom_style dipole
		dimension 2

		lattice sq2 0.7
		Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
		region box block 0 10 0 10 -0.5 0.5
		create_box 1 box
		Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
		2 by 2 by 1 processor grid
		create_atoms 1 box
		Created 200 atoms

		mass 1 1.0
		shape 1 1 1 1
		dipole 1 0.75
		set group all dipole/random 98934
		200 settings made for dipole/random

		velocity all create 0.0 87287 mom no

		pair_style dipole/cut 2.5
		pair_coeff * * 1.0 1.0

		neighbor 0.3 bin
		neigh_modify delay 0

		fix 1 all nve/dipole
		fix 2 all enforce2d

		timestep 0.005

		thermo_style dipole
		thermo 500

		dump 1 all custom 200 dump.dipole tag type x y z mux muy muz

		run 10000
		Memory usage per processor = 2.32239 Mbytes
		Step Temp E_pair RotKEdip TotEng Press
		0 0 -2.1284412 0 -2.1284412 -0.98973217
		500 0.38229437 -2.703408 0.24548268 -2.3239808 -0.073894217
		1000 0.41156476 -2.7426733 0.25757681 -2.3341953 0.05919685
		1500 0.43191585 -2.8089326 0.33203347 -2.3802561 -0.16059384
		2000 0.43337741 -2.7836977 0.30755109 -2.3535707 -0.050258895
		2500 0.41025746 -2.7704617 0.31976882 -2.3632812 -0.040387583
		3000 0.4343462 -2.7853843 0.32540887 -2.3542957 -0.040773878
		3500 0.4516216 -2.7378372 0.25848559 -2.2896027 0.01498558
		4000 0.46812215 -2.7531454 0.25653816 -2.2885341 -0.015167924
		4500 0.41857472 -2.7022096 0.27078871 -2.2867742 0.040384474
		5000 0.42275097 -2.7173978 0.28129865 -2.2978174 0.08127607
		5500 0.39689205 -2.6755268 0.28694074 -2.2816114 -0.063519745
		6000 0.40712229 -2.6810855 0.29780556 -2.2770166 -0.010331415
		6500 0.42401695 -2.7099716 0.32599472 -2.2891348 -0.080194492
		7000 0.46557586 -2.7235207 0.277596 -2.2614366 -0.025483686
		7500 0.4634213 -2.7520289 0.33385569 -2.2920833 -0.07670048
		8000 0.44330991 -2.6937045 0.28515119 -2.2537194 0.063037221
		8500 0.46501497 -2.7192191 0.31059999 -2.2576917 -0.12974997
		9000 0.48895857 -2.7113963 0.27823171 -2.2261049 -0.032792109
		9500 0.5206475 -2.7393465 0.2997953 -2.2226039 0.15436407
		10000 0.47111871 -2.6818528 0.2936091 -2.2142675 -0.18366919
		Loop time of 2.70823 on 4 procs for 10000 steps with 200 atoms

		Pair time (%) = 0.644681 (23.8045)
		Neigh time (%) = 0.0255789 (0.944486)
		Comm time (%) = 1.55045 (57.2495)
		Outpt time (%) = 0.0430555 (1.5898)
		Other time (%) = 0.444467 (16.4117)

		Nlocal: 50 ave 53 max 46 min
		Histogram: 1 0 0 0 0 1 0 1 0 1
		Nghost: 88.75 ave 91 max 86 min
		Histogram: 1 0 0 0 1 0 0 0 1 1
		Neighs: 402.25 ave 443 max 365 min
		Histogram: 1 0 0 1 0 1 0 0 0 1

		Total # of neighbors = 1609
		Ave neighs/atom = 8.045
		Neighbor list builds = 700
		Dangerous builds = 0

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