Merge branch 'master' into remove-reax-meam (d15e4b15) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+4 −1

Original line number	Diff line number	Diff line
		@@ -221,7 +221,7 @@ else()
		endif()


		set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
		set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
		set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
		set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
		validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
		@@ -856,6 +856,9 @@ if(PKG_USER-AWPMD)
		endif()

		if(PKG_USER-ATC)
		if(LAMMPS_SIZES STREQUAL BIGBIG)
		message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
		endif()
		target_link_libraries(atc ${LAPACK_LIBRARIES})
		endif()

doc/src/Manual.txt

+2 −2

Original line number	Diff line number	Diff line
		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="7 Dec 2018 version">
		<META NAME="docnumber" CONTENT="12 Dec 2018 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		:line

		LAMMPS Documentation :c,h1
		7 Dec 2018 version :c,h2
		12 Dec 2018 version :c,h2

		"What is a LAMMPS version?"_Manual_version.html

doc/src/fix_rigid_meso.txt

+4 −3

Original line number	Diff line number	Diff line
		@@ -160,7 +160,7 @@ unaffected by interactions with other particles. Note that if you
		expect a rigid body not to move or rotate by using these keywords, you
		must insure its initial center-of-mass translational or angular
		velocity is 0.0. Otherwise the initial translational or angular
		momentum the body has will persist.
		momentum, the body has, will persist.

		An xflag, yflag, or zflag set to {off} means turn off the component of
		force or torque in that dimension. A setting of {on} means turn on
		@@ -287,9 +287,10 @@ bodies. The number of columns is 28. Thus for each rigid body, 28
		values are stored: the xyz coords of the center of mass (COM), the xyz
		components of the COM velocity, the xyz components of the force acting
		on the COM, the components of the 4-vector quaternion representing the
		orientation of the rigid body, the xyz components of the angular momentum
		orientation of the rigid body, the xyz components of the angular velocity
		of the body around its COM, the xyz components of the torque acting on the
		COM, the 3 principal components of the moment of inertia and the xyz image
		COM, the 3 principal components of the moment of inertia, the xyz components
		of the angular momentum of the body around its COM, and the xyz image
		flags of the COM.

		The center of mass (COM) for each body is similar to unwrapped

doc/utils/sphinx-config/false_positives.txt

+0 −1

Original line number	Diff line number	Diff line
		@@ -63,7 +63,6 @@ aliceblue
		allocaters
		allosws
		AlO
		alond
		Alonso
		amap
		Amatrix

examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1

0 → 100644

+193 −0

Original line number	Diff line number	Diff line
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# 250 butane system for drude polarizability example (Langevin)

		units real
		boundary p p p

		atom_style full
		bond_style harmonic
		angle_style harmonic
		dihedral_style opls
		special_bonds lj/coul 0.0 0.0 0.5

		pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
		pair_modify mix geometric tail yes
		kspace_style pppm 1.0e-4

		read_data data.butane
		orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		4500 atoms
		scanning bonds ...
		5 = max bonds/atom
		scanning angles ...
		6 = max angles/atom
		scanning dihedrals ...
		9 = max dihedrals/atom
		reading bonds ...
		4250 bonds
		reading angles ...
		6000 angles
		reading dihedrals ...
		6750 dihedrals
		5 = max # of 1-2 neighbors
		8 = max # of 1-3 neighbors
		12 = max # of 1-4 neighbors
		17 = max # of special neighbors

		comm_modify vel yes

		group gBUTANE molecule 1:250
		4500 atoms in group gBUTANE
		group gCORES type 1 2 3
		3500 atoms in group gCORES
		group gDRUDES type 4 5
		1000 atoms in group gDRUDES

		pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
		pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
		pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H
		pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
		pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H
		pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H
		pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
		pair_coeff 1 * thole 1.368000
		pair_coeff 2 * thole 1.368000
		pair_coeff 4 * thole 1.368000
		pair_coeff 5 * thole 1.368000

		neighbor 2.0 bin

		variable vTEMP equal 260.0
		variable vTEMP_D equal 1.0
		variable vPRESS equal 1.0

		velocity gCORES create ${vTEMP} 12345
		velocity gCORES create 260 12345
		velocity gDRUDES create ${vTEMP_D} 12345
		velocity gDRUDES create 1 12345

		fix fDRUDE all drude C C N D D

		fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
		0 = # of size 2 clusters
		500 = # of size 3 clusters
		500 = # of size 4 clusters
		0 = # of frozen angles

		fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
		fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
		fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
		fix fNPH all nve

		compute cTEMP all temp/drude

		thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
		thermo 50

		timestep 0.5
		run 2000
		PPPM initialization ...
		using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
		G vector (1/distance) = 0.367867
		grid = 36 36 36
		stencil order = 5
		estimated absolute RMS force accuracy = 0.031354
		estimated relative force accuracy = 9.44215e-05
		using double precision FFTs
		3d grid and FFT values/proc = 79507 46656
		Rebuild special list taking Drude particles into account
		Old max number of 1-2 to 1-4 neighbors: 17
		New max number of 1-2 to 1-4 neighbors: 17 (+0)
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 10
		ghost atom cutoff = 10
		binsize = 5, bins = 8 8 8
		2 neighbor lists, perpetual/occasional/extra = 2 0 0
		(1) pair lj/cut/coul/long, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		(2) pair thole, perpetual, skip from (1)
		attributes: half, newton on
		pair build: skip
		stencil: none
		bin: none
		Per MPI rank memory allocation (min/avg/max) = 26.29 \| 26.29 \| 26.29 Mbytes
		Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2]
		0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655
		50 1.8285224 3442.9216 2047.8425 187.41713 1395.0792 844.61103 802.43438 114.10967 0 -765.532 595242.44 -594842.98 3027.409 55742.797 200.4343 152.51723
		100 3.7075663 2949.9137 1973.6229 180.62461 976.29073 358.0742 923.62856 174.43734 0 -919.88297 595306.76 -594866.72 2009.106 55742.797 229.49986 50.10998
		150 5.5383921 2885.0697 1951.4547 178.59578 933.61499 234.26452 991.10197 194.44106 0 -910.03339 595293.22 -594869.38 4963.8801 55742.797 240.13548 14.311317
		200 7.4217758 2890.343 1901.2801 174.00384 989.06297 227.57533 1077.5605 200.01467 0 -943.83325 595298.11 -594870.36 2977.5804 55742.797 237.27186 5.1150968
		250 9.2994335 2922.348 1945.2702 178.02978 977.07781 212.26144 1127.8726 194.65284 0 -984.2934 595297.59 -594871.01 1592.2372 55742.797 243.81864 2.4147813
		300 11.125204 2986.575 2013.159 184.24291 973.41608 212.85963 1130.6272 194.90599 0 -992.98724 595299.3 -594871.29 2816.8628 55742.797 252.63444 1.681279
		350 12.99769 3051.4916 1978.4541 181.06675 1073.0375 228.43411 1195.4688 205.43169 0 -982.55178 595297.25 -594871 1408.7973 55742.797 248.34887 1.4666749
		400 14.865399 3011.3983 1995.0047 182.58145 1016.3936 237.79955 1167.8185 197.49857 0 -1014.9362 595298.99 -594870.78 1456.5007 55742.797 250.45674 1.3981189
		450 16.681866 3010.262 1976.9744 180.93133 1033.2876 216.3478 1196.7189 197.65964 0 -1005.6015 595298.72 -594870.56 1296.528 55742.797 248.1869 1.4022273
		500 18.553431 3051.4554 2022.049 185.05652 1029.4064 220.84993 1196.1502 199.57249 0 -1014.3775 595298.27 -594871.05 2481.7571 55742.797 253.85835 1.3999256
		550 20.416665 3086.0021 2018.9226 184.7704 1067.0796 221.95877 1215.9767 213.3405 0 -1012.5564 595299.48 -594871.12 1694.9376 55742.797 253.47686 1.3683935
		600 22.27849 3110.9928 2030.8992 185.86649 1080.0935 220.35725 1253.9571 208.13083 0 -1030.4314 595298.96 -594870.88 -76.102661 55742.797 254.95682 1.4397403
		650 24.087152 3154.373 2024.8469 185.31258 1129.5261 221.85968 1283.352 210.69451 0 -1015.2311 595299.67 -594870.82 1280.5683 55742.797 254.20302 1.4194509
		700 25.941822 3133.85 2054.2045 187.99938 1079.6454 225.19338 1242.7819 192.54094 0 -1010.8971 595301.2 -594871.18 696.8538 55742.797 257.8878 1.4422435
		750 27.79477 3189.0815 2103.7507 192.53381 1085.3308 219.46949 1243.7676 203.10695 0 -1010.2442 595299.93 -594870.7 483.46393 55742.797 264.14441 1.3796789
		800 29.64589 3173.663 2053.4832 187.93336 1120.1799 219.59931 1256.2721 218.76191 0 -1003.0067 595299.37 -594870.81 543.09774 55742.797 257.81268 1.4005681
		850 31.44585 3221.2873 2083.5215 190.68244 1137.7658 224.0492 1276.9143 219.91997 0 -1011.193 595298.47 -594870.4 143.54962 55742.797 261.60038 1.3772624
		900 33.293605 3214.96 2053.8414 187.96614 1161.1187 222.21434 1296.0291 226.57612 0 -1013.6289 595300.61 -594870.68 473.39553 55742.797 257.85596 1.4053153
		950 35.166863 3213.1086 2123.777 194.3666 1089.3317 221.79126 1251.6851 200.63798 0 -1014.0889 595300.01 -594870.7 1206.8497 55742.797 266.62111 1.4935247
		1000 36.983663 3211.3103 2079.738 190.33618 1131.5723 225.4767 1260.2162 204.61245 0 -986.95685 595298.7 -594870.48 787.31501 55742.797 261.0928 1.4615275
		1050 38.806926 3199.3221 2095.9148 191.81667 1103.4073 212.62976 1255.417 208.36886 0 -1001.9237 595299.13 -594870.21 239.45594 55742.797 263.14173 1.4246893
		1100 40.634771 3199.8694 2067.6467 189.2296 1132.2227 235.50505 1264.2214 198.42446 0 -994.78564 595299.12 -594870.26 830.67515 55742.797 259.58627 1.4225726
		1150 42.427903 3172.4663 2083.0988 190.64376 1089.3675 209.20043 1236.7213 204.50261 0 -990.26027 595299.43 -594870.22 1355.1408 55742.797 261.54264 1.389433
		1200 44.302469 3178.2153 2055.1801 188.08866 1123.0351 230.76616 1258.2175 205.04893 0 -999.28826 595298.25 -594869.96 819.5423 55742.797 258.01926 1.4189827
		1250 46.164956 3224.5367 2108.1449 192.93596 1116.3918 235.56939 1247.0387 212.74774 0 -1007.3896 595298.16 -594869.74 -146.38102 55742.797 264.67477 1.4395372
		1300 48.015128 3286.0631 2125.3364 194.50931 1160.7267 236.69229 1272.7247 218.49151 0 -995.46842 595298.38 -594870.1 434.46496 55742.797 266.83295 1.451771
		1350 49.79655 3247.1808 2087.4518 191.04214 1159.7291 215.07571 1301.219 211.43766 0 -995.15128 595297.24 -594870.09 1501.3496 55742.797 262.07016 1.44305
		1400 51.624074 3194.7716 2041.9251 186.87557 1152.8466 236.94802 1261.0635 209.14663 0 -982.03995 595297.35 -594869.63 346.64925 55742.797 256.31352 1.5208162
		1450 53.450535 3229.6083 2087.4545 191.04239 1142.1538 246.85361 1264.077 205.22437 0 -1003.5382 595299.44 -594869.9 278.1536 55742.797 262.08335 1.4087832
		1500 55.288627 3249.6608 2089.8541 191.262 1159.8067 238.99337 1274.9502 206.61799 0 -988.99015 595297.98 -594869.75 636.34142 55742.797 262.36618 1.4595924
		1550 57.093174 3273.2213 2122.5463 194.25397 1150.675 230.16428 1274.9965 195.7686 0 -979.24728 595298.84 -594869.85 528.01943 55742.797 266.47594 1.4678006
		1600 58.978489 3288.6787 2120.7284 194.0876 1167.9503 229.10278 1274.2494 205.30619 0 -969.94195 595298.85 -594869.62 1126.6579 55742.797 266.23416 1.5026913
		1650 60.803467 3286.3327 2148.1031 196.59291 1138.2295 234.18582 1256.2009 214.69184 0 -995.41699 595298.38 -594869.81 -457.07393 55742.797 269.67989 1.4977223
		1700 62.624963 3296.9487 2092.8432 191.53556 1204.1055 238.05554 1313.8592 213.47968 0 -989.09874 595297.16 -594869.35 981.42569 55742.797 262.7423 1.4593707
		1750 64.39829 3310.3958 2097.6547 191.97591 1212.7411 243.56621 1309.681 210.07115 0 -978.63733 595297.78 -594869.72 -41.877565 55742.797 263.31945 1.5344885
		1800 66.216881 3229.7417 2079.7567 190.33789 1149.985 226.57585 1276.3941 202.60118 0 -984.26122 595298.62 -594869.94 515.97995 55742.797 261.07174 1.5239416
		1850 68.038292 3199.6375 2033.1459 186.0721 1166.4916 242.84458 1267.7768 212.87764 0 -984.52187 595296.72 -594869.21 440.77319 55742.797 255.22287 1.4839954
		1900 69.841965 3155.3872 2019.0731 184.78417 1136.3141 213.38104 1263.0105 213.0042 0 -980.43253 595296.92 -594869.57 469.76979 55742.797 253.48524 1.3965366
		1950 71.702563 3191.9366 2051.5475 187.75621 1140.3891 211.61608 1278.9441 206.1048 0 -984.04544 595297.56 -594869.79 758.07165 55742.797 257.54478 1.4655839
		2000 73.520102 3214.3938 2041.9357 186.87654 1172.4582 237.13198 1275.4194 218.0467 0 -985.25597 595296.76 -594869.64 375.81502 55742.797 256.33161 1.4761528
		Loop time of 73.5201 on 1 procs for 2000 steps with 4500 atoms

		Performance: 1.175 ns/day, 20.422 hours/ns, 27.203 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 \| 50.346 \| 50.346 \| 50.346 \| 0.0 \| 68.48
		Bond \| 3.3227 \| 3.3227 \| 3.3227 \| 0.0 \| 4.52
		Kspace \| 16.003 \| 16.003 \| 16.003 \| 0.0 \| 21.77
		Neigh \| 1.3495 \| 1.3495 \| 1.3495 \| 0.0 \| 1.84
		Comm \| 0.33013 \| 0.33013 \| 0.33013 \| 0.0 \| 0.45
		Output \| 0.0044131 \| 0.0044131 \| 0.0044131 \| 0.0 \| 0.01
		Modify \| 2.1068 \| 2.1068 \| 2.1068 \| 0.0 \| 2.87
		Other \| \| 0.05755 \| \| \| 0.08

		Nlocal: 4500 ave 4500 max 4500 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 8703 ave 8703 max 8703 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 860806 ave 860806 max 860806 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 860806
		Ave neighs/atom = 191.29
		Ave special neighs/atom = 13.3333
		Neighbor list builds = 28
		Dangerous builds = 0
		Total wall time: 0:01:13

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