update example logfiles for USER-DRUDE package (b6b81345) · Commits · 郑智淋 / lammps

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