Merge pull request #1452 from akohlmey/github-rebo-bugfix (928600a8) · Commits · 郑智淋 / lammps

doc/src/pair_airebo.txt

+9 −8

Original line number	Diff line number	Diff line
		@@ -36,7 +36,7 @@ pair_style airebo/morse 3.0
		pair_coeff * * ../potentials/CH.airebo-m H C :pre

		pair_style rebo
		pair_coeff * * ../potentials/CH.airebo H C :pre
		pair_coeff * * ../potentials/CH.rebo H C :pre

		[Description:]

		@@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
		Potential of "(Brenner)"_#Brenner. Note that this is the so-called
		2nd generation REBO from 2002, not the original REBO from 1990.
		As discussed below, 2nd generation REBO is closely related to the
		initial AIREBO; it is just a subset of the potential energy terms.
		initial AIREBO; it is just a subset of the potential energy terms
		with a few slightly different parameters

		The AIREBO potential consists of three terms:

		@@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations.
		:line

		Only a single pair_coeff command is used with the {airebo}, {airebo}
		or {rebo} style which specifies an AIREBO or AIREBO-M potential file
		with parameters for C and H. Note that the {rebo} style in LAMMPS
		uses the same AIREBO-formatted potential file. These are mapped to
		LAMMPS atom types by specifying N additional arguments after the
		filename in the pair_coeff command, where N is the number of LAMMPS
		atom types:
		or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential
		file with parameters for C and H. Note that as of LAMMPS version
		15 May 2019 the {rebo} style in LAMMPS uses its own potential
		file (CH.rebo). These are mapped to LAMMPS atom types by specifying
		N additional arguments after the filename in the pair_coeff command,
		where N is the number of LAMMPS atom types:

		filename
		N element names = mapping of AIREBO elements to atom types :ul

examples/USER/misc/kolmogorov_crespi_z/CH.airebo

deleted120000 → 0

+0 −1

Original line number	Diff line number	Diff line
		../../../../potentials/CH.airebo
		No newline at end of file

examples/USER/misc/kolmogorov_crespi_z/CH.rebo

0 → 120000

+1 −0

Original line number	Diff line number	Diff line
		../../../../potentials/CH.rebo
		No newline at end of file

examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene

+1 −1

Original line number	Diff line number	Diff line
		@@ -22,7 +22,7 @@ group adsorbant type 2
		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
		####################################################################
		pair_coeff * * rebo CH.airebo C C # chemical
		pair_coeff * * rebo CH.rebo C C # chemical
		pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
		####################################################################

examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1

deleted100644 → 0

+0 −208

Original line number	Diff line number	Diff line
		LAMMPS (8 Mar 2018)
		using 1 OpenMP thread(s) per MPI task
		# Initialization
		units metal
		boundary p p p
		atom_style atomic
		processors * * 1 # domain decomposition over x and y

		# System and atom definition
		# we use 2 atom types so that inter- and intra-layer
		# interactions can be specified separately
		read_data data.bilayer-graphene # read lammps data file
		orthogonal box = (0 0 -20) to (17.04 19.6761 40)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		256 atoms
		mass 1 12.0107 # carbon mass (g/mole) \| membrane
		mass 2 12.0107 # carbon mass (g/mole) \| adsorbate
		# Neighbor update settings
		neighbor 2.0 bin
		neigh_modify every 1
		neigh_modify delay 0
		neigh_modify check yes
		# Separate atom groups
		group membrane type 1
		128 atoms in group membrane
		group adsorbant type 2
		128 atoms in group adsorbant

		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
		####################################################################
		pair_coeff * * rebo CH.airebo C C # chemical
		Reading potential file CH.airebo with DATE: 2011-10-25
		pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
		####################################################################

		#### Simulation settings ####
		timestep 0.0001
		velocity all create 300.0 12345
		fix thermostat all nve
		compute COM1 membrane com
		compute COM2 adsorbant com
		############################

		# Output
		#dump 1 all xyz 100 trajec.xyz
		#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
		thermo 10
		thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
		thermo_modify line one format float %14.8f

		###### Run molecular dynamics ######
		run 1000
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 16
		ghost atom cutoff = 16
		binsize = 8, bins = 3 3 8
		3 neighbor lists, perpetual/occasional/extra = 3 0 0
		(1) pair rebo, perpetual
		attributes: full, newton on, ghost
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		bin: standard
		(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
		attributes: half, newton on
		pair build: skip
		stencil: none
		bin: none
		(3) neighbor class addition, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 4.998 \| 4.998 \| 4.998 Mbytes
		Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
		0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
		10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
		20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
		30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
		40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
		50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
		60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
		70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
		80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
		90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
		100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
		110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
		120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
		130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
		140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
		150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
		160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
		170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
		180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
		190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
		200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
		210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
		220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
		230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
		240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
		250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
		260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
		270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
		280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
		290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
		300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
		310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
		320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
		330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
		340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
		350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
		360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
		370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
		380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
		390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
		400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
		410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
		420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
		430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
		440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
		450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
		460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
		470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
		480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
		490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
		500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
		510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
		520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
		530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
		540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
		550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
		560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
		570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
		580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
		590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
		600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
		610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
		620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
		630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
		640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
		650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
		660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
		670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
		680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
		690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
		700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
		710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
		720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
		730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
		740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
		750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
		760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
		770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
		780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
		790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
		800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
		810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
		820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
		830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
		840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
		850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
		860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
		870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
		880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
		890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
		900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
		910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
		920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
		930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
		940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
		950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
		960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
		970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
		980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
		990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
		1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
		Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms

		Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
		99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 3.8786 \| 3.8786 \| 3.8786 \| 0.0 \| 99.41
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.010816 \| 0.010816 \| 0.010816 \| 0.0 \| 0.28
		Output \| 0.002461 \| 0.002461 \| 0.002461 \| 0.0 \| 0.06
		Modify \| 0.0051703 \| 0.0051703 \| 0.0051703 \| 0.0 \| 0.13
		Other \| \| 0.004447 \| \| \| 0.11

		Nlocal: 256 ave 256 max 256 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 1721 ave 1721 max 1721 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 37312 ave 37312 max 37312 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		FullNghs: 94592 ave 94592 max 94592 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 94592
		Ave neighs/atom = 369.5
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:00:03

Admin message