correct micelle data file without overwriting the molecule ids (1926c956) · Commits · 郑智淋 / lammps

examples/micelle/data.micelle

+1528 −1537

File changed.

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examples/micelle/log.28Feb2019.micelle-rigid.g++.1

+122 −118

Original line number	Diff line number	Diff line
		LAMMPS (28 Feb 2019)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
		using 1 OpenMP thread(s) per MPI task
		# 2d micelle simulation

		@@ -13,7 +13,7 @@ atom_style bond
		# Soft potential push-off

		read_data data.micelle
		orthogonal box = (-0.39293 -0.050929 -0.1) to (35.4639 35.8059 0.1)
		orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		1200 atoms
		@@ -25,9 +25,12 @@ read_data data.micelle
		1 = max # of 1-3 neighbors
		1 = max # of 1-4 neighbors
		2 = max # of special neighbors
		special bonds CPU = 0.000271559 secs
		read_data CPU = 0.00115585 secs
		special_bonds fene
		2 = max # of 1-2 neighbors
		2 = max # of special neighbors
		special bonds CPU = 8.39233e-05 secs

		pair_style soft 1.12246
		pair_coeff * * 0.0 1.12246
		@@ -60,54 +63,54 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.799 \| 3.799 \| 3.799 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 0.45 0.40179153 0.017198847 0.86861538 0.75625658
		50 0.4900086 0.67873245 0.060027837 1.2283605 1.3564879
		100 0.45 0.73189198 0.056737309 1.2382543 2.321972
		150 0.67879051 0.72086182 0.047167282 1.446254 2.8618146
		200 0.45 0.78767975 0.079977445 1.3172822 3.0463605
		250 0.66920583 0.70051688 0.080338407 1.4495034 3.6886758
		300 0.45 0.76847924 0.069944127 1.2880484 3.7420091
		350 0.68081034 0.62208465 0.07485122 1.3771789 4.2772161
		400 0.45 0.69469019 0.094115526 1.2384307 4.4786122
		450 0.58484619 0.64001545 0.080279506 1.3046538 4.7171436
		500 0.45 0.64066675 0.080351857 1.1706436 4.7965076
		550 0.56464426 0.57619219 0.080291646 1.2206576 4.926662
		600 0.45 0.58371075 0.088545932 1.1218817 5.0963739
		650 0.53299132 0.54564667 0.084628459 1.1628223 5.2932897
		700 0.45 0.5394553 0.10365542 1.0927357 5.3370157
		750 0.55102913 0.48080137 0.093062502 1.1244338 5.3005553
		800 0.45 0.51563293 0.1030928 1.0683507 5.5156219
		850 0.51623625 0.4768524 0.10367899 1.0963375 5.5799809
		900 0.45 0.4758065 0.098479812 1.0239113 5.6783722
		950 0.49518604 0.45196847 0.10031719 1.047059 5.8438261
		1000 0.45 0.45306784 0.094144249 0.99683709 5.8485623
		Loop time of 0.108068 on 1 procs for 1000 steps with 1200 atoms

		Performance: 3997492.279 tau/day, 9253.454 timesteps/s
		99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
		0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
		50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
		100 0.45 0.73046745 0.054836584 1.234929 2.3196516
		150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
		200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
		250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
		300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
		350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
		400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
		450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
		500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
		550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
		600 0.45 0.58193041 0.088386617 1.119942 5.131481
		650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
		700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
		750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
		800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
		850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
		900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
		950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
		1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
		Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms

		Performance: 4029800.456 tau/day, 9328.242 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 \| 0.071711 \| 0.071711 \| 0.071711 \| 0.0 \| 66.36
		Bond \| 0.0039465 \| 0.0039465 \| 0.0039465 \| 0.0 \| 3.65
		Neigh \| 0.01743 \| 0.01743 \| 0.01743 \| 0.0 \| 16.13
		Comm \| 0.0018625 \| 0.0018625 \| 0.0018625 \| 0.0 \| 1.72
		Output \| 0.00015855 \| 0.00015855 \| 0.00015855 \| 0.0 \| 0.15
		Modify \| 0.01058 \| 0.01058 \| 0.01058 \| 0.0 \| 9.79
		Other \| \| 0.00238 \| \| \| 2.20
		Pair \| 0.072035 \| 0.072035 \| 0.072035 \| 0.0 \| 67.20
		Bond \| 0.0039918 \| 0.0039918 \| 0.0039918 \| 0.0 \| 3.72
		Neigh \| 0.016078 \| 0.016078 \| 0.016078 \| 0.0 \| 15.00
		Comm \| 0.0018375 \| 0.0018375 \| 0.0018375 \| 0.0 \| 1.71
		Output \| 0.00016379 \| 0.00016379 \| 0.00016379 \| 0.0 \| 0.15
		Modify \| 0.010665 \| 0.010665 \| 0.010665 \| 0.0 \| 9.95
		Other \| \| 0.002429 \| \| \| 2.27

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 206 ave 206 max 206 min
		Nghost: 195 ave 195 max 195 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 3191 ave 3191 max 3191 min
		Neighs: 3136 ave 3136 max 3136 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 3191
		Ave neighs/atom = 2.65917
		Total # of neighbors = 3136
		Ave neighs/atom = 2.61333
		Ave special neighs/atom = 0.5
		Neighbor list builds = 99
		Neighbor list builds = 92
		Dangerous builds = 0

		unfix 3
		@@ -150,16 +153,16 @@ thermo 1000

		reset_timestep 0
		group solvent molecule 0
		0 atoms in group solvent
		750 atoms in group solvent
		group solute subtract all solvent
		1200 atoms in group solute
		450 atoms in group solute
		unfix 1
		unfix 2
		unfix 4
		fix 1 solvent nve
		fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
		fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
		151 rigid bodies with 1200 atoms
		150 rigid bodies with 450 atoms
		fix 4 all enforce2d
		run 20000
		Neighbor list info ...
		@@ -176,111 +179,112 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 5.274 \| 5.274 \| 5.274 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 0.43824398 -1.7061976 0.094144249 -1.5297 35.328657
		1000 0.44980495 -1.7618752 0.094144249 -1.5832051 -0.78239121
		2000 0.4080548 -1.7592744 0.094144249 -1.5884498 3.7941359
		3000 0.43543409 -1.7704837 0.094144249 -1.5945142 2.0801732
		4000 0.43624218 -1.7752975 0.094144249 -1.5991761 5.3401997
		5000 0.44526204 -1.7627039 0.094144249 -1.5848875 1.8074242
		6000 0.45601171 -1.7578409 0.094144249 -1.5780044 3.6999235
		7000 0.45000311 -1.7707158 0.094144249 -1.5920085 14.198063
		8000 0.49199853 -1.7647643 0.094144249 -1.5781653 1.1767602
		9000 0.42662498 -1.7719397 0.094144249 -1.5976255 1.8316615
		10000 0.44225069 -1.7704012 0.094144249 -1.5931507 4.2515329
		11000 0.54415369 -1.7634927 0.094144249 -1.5670929 7.626065
		12000 0.42501235 -1.7698463 0.094144249 -1.5958351 1.4118043
		13000 0.48382538 -1.7497323 0.094144249 -1.5646692 2.2441707
		14000 0.4376704 -1.7658795 0.094144249 -1.5894897 2.7170856
		15000 0.42644426 -1.758103 0.094144249 -1.5838228 5.6129465
		16000 0.37371943 -1.7881668 0.094144249 -1.6237944 4.0731922
		17000 0.42320956 -1.7831129 0.094144249 -1.6094406 -4.2042077
		18000 0.47319029 -1.7642512 0.094144249 -1.5811866 1.8859862
		19000 0.45117547 -1.7736983 0.094144249 -1.5947706 -1.3566752
		20000 0.48993295 -1.7820573 0.094144249 -1.5958465 -0.63347623
		Loop time of 3.56168 on 1 procs for 20000 steps with 1200 atoms

		Performance: 2425823.418 tau/day, 5615.332 timesteps/s
		0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
		1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
		2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
		3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
		4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
		5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
		6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
		7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
		8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
		9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
		10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
		11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
		12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
		13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
		14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
		15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
		16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
		17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
		18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
		19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
		20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
		Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms

		Performance: 2347175.802 tau/day, 5433.277 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 \| 1.7048 \| 1.7048 \| 1.7048 \| 0.0 \| 47.86
		Bond \| 0.079658 \| 0.079658 \| 0.079658 \| 0.0 \| 2.24
		Neigh \| 0.36319 \| 0.36319 \| 0.36319 \| 0.0 \| 10.20
		Comm \| 0.042085 \| 0.042085 \| 0.042085 \| 0.0 \| 1.18
		Output \| 0.00021696 \| 0.00021696 \| 0.00021696 \| 0.0 \| 0.01
		Modify \| 1.3169 \| 1.3169 \| 1.3169 \| 0.0 \| 36.97
		Other \| \| 0.05485 \| \| \| 1.54
		Pair \| 1.7349 \| 1.7349 \| 1.7349 \| 0.0 \| 47.13
		Bond \| 0.079483 \| 0.079483 \| 0.079483 \| 0.0 \| 2.16
		Neigh \| 0.49063 \| 0.49063 \| 0.49063 \| 0.0 \| 13.33
		Comm \| 0.049093 \| 0.049093 \| 0.049093 \| 0.0 \| 1.33
		Output \| 0.00022578 \| 0.00022578 \| 0.00022578 \| 0.0 \| 0.01
		Modify \| 1.273 \| 1.273 \| 1.273 \| 0.0 \| 34.58
		Other \| \| 0.05369 \| \| \| 1.46

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 414 ave 414 max 414 min
		Nghost: 395 ave 395 max 395 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 8824 ave 8824 max 8824 min
		Neighs: 8915 ave 8915 max 8915 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 8824
		Ave neighs/atom = 7.35333
		Total # of neighbors = 8915
		Ave neighs/atom = 7.42917
		Ave special neighs/atom = 0.5
		Neighbor list builds = 1148
		Neighbor list builds = 1580
		Dangerous builds = 0
		unfix 5
		unfix 4
		fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
		151 rigid bodies with 1200 atoms
		25.2208 = max distance from body owner to body atom
		create bodies CPU = 0.00012517 secs
		150 rigid bodies with 450 atoms
		1.04536 = max distance from body owner to body atom
		fix 4 all enforce2d
		run 20000
		Per MPI rank memory allocation (min/avg/max) = 8.642 \| 8.642 \| 8.642 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 8.633 \| 8.633 \| 8.633 Mbytes
		Step Temp E_pair E_mol TotEng Press
		20000 0.48993295 -1.7820573 0.094144249 -1.5958465 3.267595
		21000 0.42136691 -1.7767171 0.094144249 -1.6033909 1.1186996
		22000 0.42456205 -1.7606471 0.094144249 -1.5867205 2.8866506
		23000 0.48026533 -1.7693864 0.094144249 -1.5849923 7.3708907
		24000 0.51908347 -1.7748052 0.094144249 -1.5831165 -0.88177558
		25000 0.46033763 -1.7615973 0.094144249 -1.580948 7.0803034
		26000 0.48667124 -1.7625783 0.094144249 -1.5769804 -11.557404
		27000 0.45085745 -1.7833193 0.094144249 -1.6044514 6.5390499
		28000 0.47333185 -1.7561049 0.094144249 -1.5730137 -3.2587604
		29000 0.46380712 -1.7830962 0.094144249 -1.6017949 7.1120026
		30000 0.41845082 -1.7808054 0.094144249 -1.6080272 3.6435588
		31000 0.510966 -1.7649896 0.094144249 -1.5748263 1.4979844
		32000 0.42169482 -1.7623593 0.094144249 -1.5889716 2.6130718
		33000 0.43724881 -1.769415 0.094144249 -1.5931044 1.1205627
		34000 0.43753147 -1.7878022 0.094144249 -1.6114385 9.0463054
		35000 0.44230686 -1.7554417 0.094144249 -1.5781806 3.776513
		36000 0.39564972 -1.7614398 0.094144249 -1.5929464 4.6243057
		37000 0.39176208 -1.7586072 0.094144249 -1.5908443 -2.1444581
		38000 0.4601972 -1.7727349 0.094144249 -1.5921119 9.513042
		39000 0.42107042 -1.7703643 0.094144249 -1.5970939 5.3409161
		40000 0.45100889 -1.7794839 0.094144249 -1.6005876 -8.2877164
		Loop time of 3.5613 on 1 procs for 20000 steps with 1200 atoms

		Performance: 2426077.738 tau/day, 5615.921 timesteps/s
		99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
		20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
		21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
		22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
		23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
		24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
		25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
		26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
		27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
		28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
		29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
		30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
		31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
		32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
		33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
		34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
		35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
		36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
		37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
		38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
		39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
		40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
		Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms

		Performance: 2341388.948 tau/day, 5419.882 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 \| 1.7113 \| 1.7113 \| 1.7113 \| 0.0 \| 48.05
		Bond \| 0.079594 \| 0.079594 \| 0.079594 \| 0.0 \| 2.23
		Neigh \| 0.36249 \| 0.36249 \| 0.36249 \| 0.0 \| 10.18
		Comm \| 0.042057 \| 0.042057 \| 0.042057 \| 0.0 \| 1.18
		Output \| 0.00020933 \| 0.00020933 \| 0.00020933 \| 0.0 \| 0.01
		Modify \| 1.3102 \| 1.3102 \| 1.3102 \| 0.0 \| 36.79
		Other \| \| 0.05553 \| \| \| 1.56
		Pair \| 1.756 \| 1.756 \| 1.756 \| 0.0 \| 47.59
		Bond \| 0.079221 \| 0.079221 \| 0.079221 \| 0.0 \| 2.15
		Neigh \| 0.49085 \| 0.49085 \| 0.49085 \| 0.0 \| 13.30
		Comm \| 0.048317 \| 0.048317 \| 0.048317 \| 0.0 \| 1.31
		Output \| 0.0002315 \| 0.0002315 \| 0.0002315 \| 0.0 \| 0.01
		Modify \| 1.2616 \| 1.2616 \| 1.2616 \| 0.0 \| 34.19
		Other \| \| 0.05386 \| \| \| 1.46

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 405 ave 405 max 405 min
		Nghost: 393 ave 393 max 393 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 8806 ave 8806 max 8806 min
		Neighs: 9091 ave 9091 max 9091 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 8806
		Ave neighs/atom = 7.33833
		Total # of neighbors = 9091
		Ave neighs/atom = 7.57583
		Ave special neighs/atom = 0.5
		Neighbor list builds = 1149
		Neighbor list builds = 1582
		Dangerous builds = 0
		Total wall time: 0:00:07

examples/micelle/log.28Feb2019.micelle-rigid.g++.4

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examples/micelle/log.28Feb2019.micelle.g++.1

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examples/micelle/log.28Feb2019.micelle.g++.4

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