(e3fa1c4e) · Commits · 郑智淋 / lammps

examples/colloid/in.colloid

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Original line number	Diff line number	Diff line
		# Big colloid particles and small LJ particles

		units lj
		atom_style atomic
		dimension 2

		lattice sq 0.01
		region box block 0 30 0 30 -0.5 0.5
		create_box 2 box
		create_atoms 1 box

		set group all type/fraction 2 0.96 23984

		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

examples/crack/log.crack.12Feb07.liberty.4

deleted100644 → 0

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Original line number	Diff line number	Diff line
		LAMMPS (12 Feb 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 box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
		2 by 2 by 1 processor grid
		create_atoms 1
		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 leftupper atom 2
		820 settings made
		set leftlower atom 3
		841 settings made
		set lower atom 4
		302 settings made
		set upper atom 5
		302 settings made

		# initial velocities

		compute new mobile temp
		velocity mobile create 0.01 887723 temp new
		velocity upper set 0.0 0.02 0.0
		velocity mobile ramp vy 0.0 0.02 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 1000
		thermo_modify temp new

		neigh_modify exclude type 2 3
		dump 1 all atom 250 dump.crack
		run 50000
		Memory usage per processor = 1.59725 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.010256158 -3.2595015 0 -3.2500081 -0.10145141 4792.6107
		1000 0.0050480673 -3.2546391 0 -3.2499665 -0.12639136 4792.6107
		2000 0.0051369915 -3.2543578 0 -3.2496028 -0.15975041 4807.2492
		3000 0.0052553075 -3.2540343 0 -3.2491699 -0.1774021 4810.8238
		4000 0.0050641166 -3.2533514 0 -3.2486639 -0.19022921 4811.9955
		5000 0.0050025515 -3.2525683 0 -3.2479378 -0.24015028 4816.2645
		6000 0.0049701482 -3.2516756 0 -3.2470751 -0.30916368 4828.9736
		7000 0.0051250335 -3.2507402 0 -3.2459963 -0.39169622 4833.0704
		8000 0.0048713476 -3.2493641 0 -3.2448551 -0.47693724 4840.7084
		9000 0.0049779793 -3.2481153 0 -3.2435076 -0.53299012 4846.9925
		10000 0.0049128574 -3.2466686 0 -3.2421212 -0.55373718 4857.8418
		11000 0.0049168986 -3.2450986 0 -3.2405474 -0.55984041 4861.948
		12000 0.0048612336 -3.2434103 0 -3.2389106 -0.58141697 4864.2222
		13000 0.0047721181 -3.2414759 0 -3.2370587 -0.62552646 4869.2639
		14000 0.0048830775 -3.2396196 0 -3.2350997 -0.69800852 4875.2845
		15000 0.0048743586 -3.2375595 0 -3.2330476 -0.76818454 4889.0238
		16000 0.0046772021 -3.2352919 0 -3.2309626 -0.82750427 4897.7014
		17000 0.0047699454 -3.2330635 0 -3.2286483 -0.8579342 4904.3594
		18000 0.0047753426 -3.2307014 0 -3.2262813 -0.86808974 4910.4271
		19000 0.0047514879 -3.2281706 0 -3.2237725 -0.85125679 4912.8684
		20000 0.0048479568 -3.2256981 0 -3.2212107 -0.83903361 4916.6492
		21000 0.0050005972 -3.223304 0 -3.2186754 -0.86141301 4923.3107
		22000 0.0051837721 -3.2210129 0 -3.2162147 -0.91497358 4935.0337
		23000 0.0055014883 -3.2187173 0 -3.213625 -0.98259066 4945.2474
		24000 0.0059415321 -3.2164221 0 -3.2109225 -1.0173765 4957.1622
		25000 0.0064260911 -3.2142138 0 -3.2082656 -0.99854249 4959.1051
		26000 0.0068764456 -3.2118739 0 -3.2055089 -0.96174337 4961.1023
		27000 0.0067647514 -3.2089962 0 -3.2027346 -0.91577995 4957.1713
		28000 0.0073747742 -3.2067583 0 -3.199932 -0.9190562 4964.7136
		29000 0.0081414686 -3.2046855 0 -3.1971496 -0.97705845 4980.1961
		30000 0.0088053861 -3.2024749 0 -3.1943244 -0.99081318 4997.4212
		31000 0.0093650101 -3.2005673 0 -3.1918989 -1.0220683 5011.6892
		32000 0.0098581693 -3.1984747 0 -3.1893498 -1.0266826 5014.6599
		33000 0.011028173 -3.1969382 0 -3.1867302 -0.94832256 5010.2518
		34000 0.011643915 -3.1949468 0 -3.184169 -0.90746422 5017.2254
		35000 0.01332772 -3.1938256 0 -3.1814891 -0.85591111 5047.1343
		36000 0.014454124 -3.1918323 0 -3.1784532 -0.86634436 5054.2179
		37000 0.016378188 -3.190944 0 -3.175784 -0.92602308 5077.4837
		38000 0.017843754 -3.1898052 0 -3.1732887 -0.90546324 5086.0006
		39000 0.019366756 -3.1887586 0 -3.1708323 -0.80190332 5089.7603
		40000 0.022135202 -3.1894278 0 -3.168939 -0.71192011 5093.5652
		41000 0.024807374 -3.1902712 0 -3.1673089 -0.629612 5095.3221
		42000 0.027696152 -3.1913199 0 -3.1656837 -0.65566924 5086.8449
		43000 0.028906545 -3.1904171 0 -3.1636605 -0.62599838 5095.1026
		44000 0.029856229 -3.1894006 0 -3.161765 -0.63227312 5109.8945
		45000 0.031334749 -3.1888949 0 -3.1598907 -0.62759443 5122.9902
		46000 0.034602854 -3.1903219 0 -3.1582927 -0.67305941 5123.8907
		47000 0.034415071 -3.1883711 0 -3.1565157 -0.67895291 5133.6318
		48000 0.035822122 -3.188003 0 -3.1548452 -0.56873296 5146.4656
		49000 0.035461417 -3.1863792 0 -3.1535553 -0.49114989 5146.0215
		50000 0.036039942 -3.1854474 0 -3.152088 -0.47443899 5165.9937
		Loop time of 71.7721 on 4 procs for 50000 steps with 8141 atoms

		Pair time (%) = 45.6852 (63.6532)
		Neigh time (%) = 0.910263 (1.26827)
		Comm time (%) = 11.0603 (15.4103)
		Outpt time (%) = 3.16426 (4.40877)
		Other time (%) = 10.9521 (15.2595)

		Nlocal: 2035.25 ave 2093 max 1983 min
		Histogram: 1 0 0 1 0 1 0 0 0 1
		Nghost: 201.5 ave 246 max 141 min
		Histogram: 1 0 0 1 0 0 0 0 0 2
		Neighs: 17745.5 ave 18295 max 17485 min
		Histogram: 2 1 0 0 0 0 0 0 0 1

		Total # of neighbors = 70982
		Ave neighs/atom = 8.71908
		Neighbor list builds = 491
		Dangerous builds = 0

examples/crack/log.crack.12Feb07.linux.1

deleted100644 → 0

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Original line number	Diff line number	Diff line
		LAMMPS (12 Feb 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 box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
		1 by 1 by 1 processor grid
		create_atoms 1
		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 leftupper atom 2
		820 settings made
		set leftlower atom 3
		841 settings made
		set lower atom 4
		302 settings made
		set upper atom 5
		302 settings made

		# initial velocities

		compute new mobile temp
		velocity mobile create 0.01 887723 temp new
		velocity upper set 0.0 0.02 0.0
		velocity mobile ramp vy 0.0 0.02 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 1000
		thermo_modify temp new

		neigh_modify exclude type 2 3
		dump 1 all atom 250 dump.crack
		run 50000
		Memory usage per processor = 2.04243 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 0.010233422 -3.2595015 0 -3.2500292 -0.10147524 4792.6107
		1000 0.0051057052 -3.2546357 0 -3.2499098 -0.13099352 4792.6107
		2000 0.0051305159 -3.2543693 0 -3.2496204 -0.16341482 4807.4758
		3000 0.005186568 -3.2539935 0 -3.2491927 -0.17782954 4808.2338
		4000 0.005087842 -3.2533474 0 -3.248638 -0.18347851 4814.6291
		5000 0.004952798 -3.2525326 0 -3.2479482 -0.23680218 4819.1809
		6000 0.004991209 -3.2516461 0 -3.2470261 -0.30814679 4826.0224
		7000 0.004944807 -3.2506197 0 -3.2460426 -0.39136722 4830.7072
		8000 0.0049376929 -3.2494443 0 -3.2448739 -0.48674075 4839.3787
		9000 0.0050078092 -3.2482053 0 -3.24357 -0.53039175 4853.1439
		10000 0.004983781 -3.2466688 0 -3.2420557 -0.55385151 4857.416
		11000 0.0049723432 -3.2451304 0 -3.2405279 -0.56009417 4862.5452
		12000 0.0049013912 -3.243408 0 -3.2388712 -0.57381742 4865.356
		13000 0.0048043804 -3.2415478 0 -3.2371007 -0.62822628 4866.3058
		14000 0.0048263329 -3.2395963 0 -3.2351289 -0.69278151 4872.0789
		15000 0.0047872575 -3.2375073 0 -3.2330761 -0.77081332 4885.8904
		16000 0.0047945553 -3.2353167 0 -3.2308787 -0.82826028 4893.1664
		17000 0.0047216486 -3.2330128 0 -3.2286423 -0.86086905 4902.0617
		18000 0.0047886085 -3.2306714 0 -3.226239 -0.86709584 4912.8232
		19000 0.0048029287 -3.2282267 0 -3.223781 -0.8478792 4914.5926
		20000 0.0049477774 -3.22582 0 -3.2212403 -0.83551748 4917.3514
		21000 0.0050097792 -3.2233599 0 -3.2187228 -0.83827951 4924.4496
		22000 0.0052037073 -3.2210367 0 -3.21622 -0.87712941 4935.4747
		23000 0.005250599 -3.2186209 0 -3.2137608 -0.95723098 4947.854
		24000 0.0056583383 -3.2164899 0 -3.2112524 -0.99733057 4959.3194
		25000 0.006177144 -3.2143646 0 -3.2086469 -0.99156085 4966.2512
		26000 0.0065570098 -3.2120894 0 -3.2060201 -0.94420666 4960.9584
		27000 0.0065182894 -3.2093666 0 -3.2033331 -0.87993179 4961.9079
		28000 0.0068038044 -3.2067846 0 -3.2004869 -0.86598793 4967.889
		29000 0.0077170662 -3.2049416 0 -3.1977985 -0.91334819 4981.938
		30000 0.0081816546 -3.2027043 0 -3.1951312 -0.9653003 4996.292
		31000 0.0089120184 -3.2008682 0 -3.192619 -0.99183522 5012.9271
		32000 0.0095675926 -3.1988646 0 -3.1900086 -0.98991289 5018.881
		33000 0.010803233 -3.1974474 0 -3.1874477 -0.94112056 5012.4944
		34000 0.011158338 -3.195224 0 -3.1848955 -0.8851475 5006.3799
		35000 0.011756558 -3.193118 0 -3.1822359 -0.83787524 5002.794
		36000 0.011908028 -3.1908083 0 -3.179786 -0.82041394 5013.2137
		37000 0.014248791 -3.1903606 0 -3.1771716 -0.86591483 5045.4357
		38000 0.015514642 -3.1889367 0 -3.1745759 -0.84629532 5058.8659
		39000 0.017625744 -3.1886096 0 -3.1722948 -0.72912473 5086.8791
		40000 0.020166221 -3.1891916 0 -3.1705253 -0.57976268 5092.6354
		41000 0.024585629 -3.191961 0 -3.169204 -0.45986861 5092.2489
		42000 0.025792679 -3.191911 0 -3.1680367 -0.41104431 5084.743
		43000 0.027413976 -3.1918738 0 -3.1664988 -0.317039 5103.4238
		44000 0.029084803 -3.1924106 0 -3.165489 -0.35382128 5093.6381
		45000 0.028426053 -3.1910339 0 -3.1647221 -0.40685905 5115.0911
		46000 0.028866755 -3.190439 0 -3.1637193 -0.44541816 5121.2964
		47000 0.02908918 -3.189657 0 -3.1627313 -0.4265388 5149.429
		48000 0.028710143 -3.1882276 0 -3.1616528 -0.45494173 5166.6376
		49000 0.03082438 -3.1885404 0 -3.1600086 -0.4068 5164.3287
		50000 0.032521821 -3.1887517 0 -3.1586487 -0.31047628 5170.302
		Loop time of 449.517 on 1 procs for 50000 steps with 8141 atoms

		Pair time (%) = 363.166 (80.7903)
		Neigh time (%) = 6.23528 (1.38711)
		Comm time (%) = 0.552309 (0.122867)
		Outpt time (%) = 7.92898 (1.76389)
		Other time (%) = 71.6341 (15.9358)

		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: 70714 ave 70714 max 70714 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 70714
		Ave neighs/atom = 8.68616
		Neighbor list builds = 488
		Dangerous builds = 0

examples/dipole/in.dipole

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+35 −0

Original line number	Diff line number	Diff line
		# Point dipoles in a 2d box

		units lj
		atom_style dipole
		dimension 2

		lattice sq2 0.7
		region box block 0 10 0 10 -0.5 0.5
		create_box 1 box
		create_atoms 1 box

		mass 1 1.0
		shape 1 1 1 1
		dipole 1 0.75
		set group all dipole/random 98934

		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

examples/ellipse/in.ellipse

0 → 100644

+51 −0

Original line number	Diff line number	Diff line
		# Ellipsoids in LJ background fluid

		units lj
		atom_style ellipsoid
		dimension 2

		lattice sq 0.02
		region box block 0 20 0 20 -0.5 0.5
		create_box 2 box
		create_atoms 1 box

		set group all type/fraction 2 0.1 95392
		set group all quat/random 18238

		mass 1 1.0
		mass 2 1.5
		shape 1 1 1 1
		shape 2 3 1 1

		compute rot all temp/asphere
		velocity all create 2.4 87287 loop geom

		pair_style gayberne 1.0 3.0 1.0 4.0
		pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
		pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
		pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0

		neighbor 0.8 bin

		thermo_style custom step c_rot epair etotal press vol
		thermo 100

		timestep 0.002

		dump 1 all custom 100 dump.ellipse &
		tag type x y z quatw quati quatj quatk

		fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
		fix 2 all enforce2d

		# equilibrate to shrink box around dilute system

		run 2000

		# run dynamics on dense system

		unfix 1
		fix 1 all nve/asphere

		run 2000

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