update micelle example for improved reproducibility (778537e7) · Commits · 郑智淋 / lammps

examples/micelle/in.micelle

+2 −2

Original line number	Diff line number	Diff line
		@@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246
		pair_coeff 2 3 1.0 0.88 1.12246
		pair_coeff 2 4 1.0 0.75 1.12246

		thermo 1000
		thermo 50

		#dump 1 all atom 2000 dump.micelle

		@@ -69,4 +69,4 @@ thermo 1000
		#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

		reset_timestep 0
		run 60000
		run 1000

examples/micelle/in.micelle-rigid

0 → 100644

+87 −0

Original line number	Diff line number	Diff line
		# 2d micelle simulation

		dimension 2

		neighbor 0.3 bin
		neigh_modify delay 5

		atom_style bond

		# Soft potential push-off

		read_data data.micelle
		special_bonds fene

		pair_style soft 1.12246
		pair_coeff * * 0.0 1.12246

		bond_style harmonic
		bond_coeff 1 50.0 0.75

		velocity all create 0.45 2349852

		variable prefactor equal ramp(1.0,20.0)

		fix 1 all nve
		fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
		fix 3 all adapt 1 pair soft a * * v_prefactor
		fix 4 all enforce2d

		thermo 50
		run 500

		unfix 3

		# Main run

		pair_style lj/cut 2.5

		# solvent/head - full-size and long-range

		pair_coeff 1 1 1.0 1.0 2.5
		pair_coeff 2 2 1.0 1.0 2.5
		pair_coeff 1 2 1.0 1.0 2.5

		# tail/tail - size-averaged and long-range

		pair_coeff 3 3 1.0 0.75 2.5
		pair_coeff 4 4 1.0 0.50 2.5
		pair_coeff 3 4 1.0 0.67 2.5

		# solvent/tail - full-size and repulsive

		pair_coeff 1 3 1.0 1.0 1.12246
		pair_coeff 1 4 1.0 1.0 1.12246

		# head/tail - size-averaged and repulsive

		pair_coeff 2 3 1.0 0.88 1.12246
		pair_coeff 2 4 1.0 0.75 1.12246

		thermo 50

		#dump 1 all atom 2000 dump.micelle

		#dump 2 all image 2000 image.*.jpg type type zoom 1.6
		#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

		#dump 3 all movie 2000 movie.mpg type type zoom 1.6
		#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75

		reset_timestep 0
		group solvent molecule 0
		group solute subtract all solvent
		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
		fix 4 all enforce2d
		run 500
		unfix 2
		unfix 4
		unfix 5
		fix 5 solute rigid/small molecule
		fix 4 all enforce2d
		run 500

examples/micelle/log.28Feb2019.micelle.rigid.g++.1→examples/micelle/log.29Mar2019.micelle-rigid.g++.1

+260 −0

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:88)
		LAMMPS (29 Mar 2019)
		using 1 OpenMP thread(s) per MPI task
		# 2d micelle simulation

		@@ -25,12 +24,12 @@ 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 CPU = 0.000473022 secs
		read_data CPU = 0.0024147 secs
		special_bonds fene
		2 = max # of 1-2 neighbors
		2 = max # of special neighbors
		special bonds CPU = 8.39233e-05 secs
		special bonds CPU = 0.00022316 secs

		pair_style soft 1.12246
		pair_coeff * * 0.0 1.12246
		@@ -48,7 +47,7 @@ fix 3 all adapt 1 pair soft a * * v_prefactor
		fix 4 all enforce2d

		thermo 50
		run 1000
		run 500
		Neighbor list info ...
		update every 1 steps, delay 5 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		@@ -64,53 +63,43 @@ Neighbor list info ...
		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 0.40003481 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
		50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
		100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
		150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
		200 0.45 1.01454 0.10663502 1.5708 4.7598476
		250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
		300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
		350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
		400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
		450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
		500 0.45 0.66669513 0.13695201 1.2532721 6.807146
		Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms

		Performance: 2093802.885 tau/day, 4846.766 timesteps/s
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.072035 \| 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
		Pair \| 0.068308 \| 0.068308 \| 0.068308 \| 0.0 \| 66.21
		Bond \| 0.004235 \| 0.004235 \| 0.004235 \| 0.0 \| 4.11
		Neigh \| 0.014069 \| 0.014069 \| 0.014069 \| 0.0 \| 13.64
		Comm \| 0.0019219 \| 0.0019219 \| 0.0019219 \| 0.0 \| 1.86
		Output \| 0.00017262 \| 0.00017262 \| 0.00017262 \| 0.0 \| 0.17
		Modify \| 0.011728 \| 0.011728 \| 0.011728 \| 0.0 \| 11.37
		Other \| \| 0.002726 \| \| \| 2.64

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 195 ave 195 max 195 min
		Nghost: 197 ave 197 max 197 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 3136 ave 3136 max 3136 min
		Neighs: 3094 ave 3094 max 3094 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 3136
		Ave neighs/atom = 2.61333
		Total # of neighbors = 3094
		Ave neighs/atom = 2.57833
		Ave special neighs/atom = 0.5
		Neighbor list builds = 92
		Neighbor list builds = 52
		Dangerous builds = 0

		unfix 3
		@@ -141,7 +130,7 @@ pair_coeff 1 4 1.0 1.0 1.12246
		pair_coeff 2 3 1.0 0.88 1.12246
		pair_coeff 2 4 1.0 0.75 1.12246

		thermo 1000
		thermo 50

		#dump 1 all atom 2000 dump.micelle

		@@ -164,7 +153,7 @@ 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
		150 rigid bodies with 450 atoms
		fix 4 all enforce2d
		run 20000
		run 500
		Neighbor list info ...
		update every 1 steps, delay 5 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		@@ -179,112 +168,93 @@ 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 0.44603578 -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
		0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
		50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
		100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
		150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
		200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
		250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
		300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
		350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
		400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
		450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
		500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
		Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms

		Performance: 1208012.705 tau/day, 2796.326 timesteps/s
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.7349 \| 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
		Pair \| 0.086131 \| 0.086131 \| 0.086131 \| 0.0 \| 48.17
		Bond \| 0.0042472 \| 0.0042472 \| 0.0042472 \| 0.0 \| 2.38
		Neigh \| 0.021317 \| 0.021317 \| 0.021317 \| 0.0 \| 11.92
		Comm \| 0.0025985 \| 0.0025985 \| 0.0025985 \| 0.0 \| 1.45
		Output \| 0.000175 \| 0.000175 \| 0.000175 \| 0.0 \| 0.10
		Modify \| 0.061408 \| 0.061408 \| 0.061408 \| 0.0 \| 34.34
		Other \| \| 0.00293 \| \| \| 1.64

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 395 ave 395 max 395 min
		Nghost: 416 ave 416 max 416 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 8915 ave 8915 max 8915 min
		Neighs: 8769 ave 8769 max 8769 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 8915
		Ave neighs/atom = 7.42917
		Total # of neighbors = 8769
		Ave neighs/atom = 7.3075
		Ave special neighs/atom = 0.5
		Neighbor list builds = 1580
		Dangerous builds = 0
		unfix 5
		Neighbor list builds = 47
		Dangerous builds = 2
		unfix 2
		unfix 4
		fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
		create bodies CPU = 0.00012517 secs
		unfix 5
		fix 5 solute rigid/small molecule
		create bodies CPU = 0.00015378 secs
		150 rigid bodies with 450 atoms
		1.04536 = max distance from body owner to body atom
		1.30435 = max distance from body owner to body atom
		fix 4 all enforce2d
		run 20000
		Per MPI rank memory allocation (min/avg/max) = 8.633 \| 8.633 \| 8.633 Mbytes
		run 500
		Per MPI rank memory allocation (min/avg/max) = 8.64 \| 8.64 \| 8.64 Mbytes
		Step Temp E_pair E_mol TotEng Press
		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
		500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
		550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
		600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
		650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
		700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
		750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
		800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
		850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
		900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
		950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
		1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
		Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms

		Performance: 1297278.008 tau/day, 3002.958 timesteps/s
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.756 \| 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
		Pair \| 0.085767 \| 0.085767 \| 0.085767 \| 0.0 \| 51.51
		Bond \| 0.0042562 \| 0.0042562 \| 0.0042562 \| 0.0 \| 2.56
		Neigh \| 0.018039 \| 0.018039 \| 0.018039 \| 0.0 \| 10.83
		Comm \| 0.0024002 \| 0.0024002 \| 0.0024002 \| 0.0 \| 1.44
		Output \| 0.00018239 \| 0.00018239 \| 0.00018239 \| 0.0 \| 0.11
		Modify \| 0.052717 \| 0.052717 \| 0.052717 \| 0.0 \| 31.66
		Other \| \| 0.003141 \| \| \| 1.89

		Nlocal: 1200 ave 1200 max 1200 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 393 ave 393 max 393 min
		Nghost: 415 ave 415 max 415 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 9091 ave 9091 max 9091 min
		Neighs: 8743 ave 8743 max 8743 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 9091
		Ave neighs/atom = 7.57583
		Total # of neighbors = 8743
		Ave neighs/atom = 7.28583
		Ave special neighs/atom = 0.5
		Neighbor list builds = 1582
		Neighbor list builds = 40
		Dangerous builds = 0
		Total wall time: 0:00:07
		Total wall time: 0:00:00

examples/micelle/log.28Feb2019.micelle.rigid.g++.4→examples/micelle/log.29Mar2019.micelle-rigid.g++.4

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examples/micelle/log.28Feb2019.micelle.g++.1→examples/micelle/log.29Mar2019.micelle.g++.1

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