add example for gREM (26870f22) · Commits · 郑智淋 / lammps

examples/USER/misc/grem/lj-single/in.gREM

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Original line number	Diff line number	Diff line
		# LJ particles
		variable T0 equal 300.0
		variable press equal 0.0

		units real
		atom_style full
		pair_style lj/cut 5.0

		read_data "lj.data"

		thermo 10
		thermo_style custom step temp pe etotal press vol

		timestep 1.0

		fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
		fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
		thermo_modify press fxgREM_press
		fix_modify fxnvt press fxgREM_press
		run 1000

		#write_data lj-out.data

examples/USER/misc/grem/lj-single/lj.data

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+1022 −0

File added.

Preview size limit exceeded, changes collapsed.

examples/USER/misc/grem/lj-single/log.gREM.9Nov16.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (9 Nov 2016)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task
		# LJ particles
		variable T0 equal 300.0
		variable press equal 0.0

		units real
		atom_style full
		pair_style lj/cut 5.0

		read_data "lj.data"
		orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		500 atoms
		reading velocities ...
		500 velocities
		0 = max # of 1-2 neighbors
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors

		thermo 10
		thermo_style custom step temp pe etotal press vol

		timestep 1.0

		fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
		fix fxgREM all grem 400 -.01 -30000 300 ${press}
		fix fxgREM all grem 400 -.01 -30000 300 0
		fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
		thermo_modify press fxgREM_press
		fix_modify fxnvt press fxgREM_press
		run 1000
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 7
		ghost atom cutoff = 7
		binsize = 3.5 -> bins = 7 7 7
		Memory usage per processor = 5.37943 Mbytes
		Step Temp PotEng TotEng Press Volume
		0 305.69499 -3177.6423 -2722.9442 -91.741776 11950.115
		10 312.30124 -3182.2257 -2717.7013 -203.95075 11950.113
		20 314.94567 -3186.456 -2717.9982 -265.56737 11950.108
		30 312.229 -3183.7641 -2719.3472 -196.90499 11950.097
		40 305.94068 -3180.7085 -2725.6449 -92.562221 11950.083
		50 300.42281 -3176.5838 -2729.7277 10.896769 11950.066
		60 299.16747 -3174.1939 -2729.205 50.094171 11950.05
		70 301.65965 -3176.0918 -2727.396 0.096901939 11950.035
		80 304.77876 -3178.2699 -2724.9346 -64.001022 11950.019
		90 305.60598 -3178.9517 -2724.386 -93.672879 11950.003
		100 303.8005 -3177.5156 -2725.6354 -74.516709 11949.985
		110 300.86776 -3175.4773 -2727.9593 -34.22655 11949.965
		120 298.70177 -3175.6488 -2731.3526 -19.014898 11949.944
		130 298.39686 -3176.3792 -2732.5365 -21.293245 11949.923
		140 300.00669 -3177.7032 -2731.466 -40.992937 11949.902
		150 301.85665 -3178.1312 -2729.1423 -45.715505 11949.88
		160 301.20597 -3177.3218 -2729.3007 -10.104082 11949.857
		170 297.01134 -3172.7462 -2730.9643 99.298381 11949.833
		180 291.279 -3168.3513 -2735.0958 219.47549 11949.812
		190 287.13954 -3165.1287 -2738.0304 309.36947 11949.796
		200 286.57735 -3165.2951 -2739.033 323.96954 11949.786
		210 289.83941 -3167.8245 -2736.7103 271.77305 11949.783
		220 296.12858 -3171.8054 -2731.3366 172.4056 11949.785
		230 303.82424 -3176.3108 -2724.3952 56.711479 11949.791
		240 309.95738 -3180.9789 -2719.9408 -40.992898 11949.798
		250 312.0405 -3182.3473 -2718.2107 -57.591676 11949.805
		260 309.65444 -3181.0587 -2720.4712 3.3540332 11949.81
		270 304.40001 -3176.5798 -2723.8078 130.77028 11949.816
		280 298.65985 -3174.1505 -2729.9166 237.63562 11949.825
		290 294.78709 -3170.9701 -2732.4966 326.94924 11949.838
		300 294.03216 -3169.9567 -2732.6062 349.85486 11949.859
		310 296.44397 -3172.8519 -2731.914 284.80897 11949.886
		320 301.41027 -3175.9697 -2727.6447 179.4647 11949.92
		330 307.88911 -3181.2615 -2723.2998 24.702414 11949.957
		340 314.73138 -3186.0047 -2717.8656 -132.6263 11949.995
		350 320.55591 -3187.8509 -2711.0483 -245.88468 11950.031
		360 323.50274 -3188.9994 -2707.8136 -314.73676 11950.062
		370 321.61539 -3187.1233 -2708.7448 -293.17446 11950.086
		380 314.37275 -3181.484 -2713.8784 -169.00448 11950.104
		390 303.54884 -3174.1675 -2722.6616 12.923999 11950.119
		400 293.40432 -3167.0348 -2730.6181 187.6624 11950.135
		410 288.46351 -3165.273 -2736.2054 252.20051 11950.154
		420 290.31387 -3168.604 -2736.7841 193.73816 11950.178
		430 296.35519 -3173.09 -2732.2841 81.521847 11950.207
		440 301.92973 -3175.4344 -2726.3368 -1.8329439 11950.237
		450 303.76205 -3176.777 -2724.9539 -35.002096 11950.267
		460 301.71619 -3174.2731 -2725.4932 14.977875 11950.296
		470 298.92404 -3172.9921 -2728.3652 64.224747 11950.326
		480 298.80164 -3172.5329 -2728.0881 82.781347 11950.358
		490 302.71589 -3175.3703 -2725.1034 27.223049 11950.39
		500 309.10665 -3179.3013 -2719.5285 -65.460658 11950.424
		510 314.36408 -3183.2854 -2715.6927 -151.19245 11950.456
		520 315.71154 -3183.5328 -2713.9358 -163.19151 11950.485
		530 313.31886 -3182.2521 -2716.214 -125.5741 11950.511
		540 309.81847 -3178.9358 -2718.1043 -55.55841 11950.534
		550 308.29687 -3177.837 -2719.2688 -24.39371 11950.556
		560 308.75927 -3176.3265 -2717.0705 0.93689833 11950.578
		570 307.52811 -3175.8145 -2718.3897 35.502429 11950.6
		580 301.75074 -3173.1208 -2724.2894 136.29625 11950.622
		590 292.37743 -3165.5806 -2730.6913 319.75957 11950.648
		600 283.57627 -3159.8617 -2738.0635 471.28045 11950.68
		610 279.85172 -3157.4557 -2741.1975 530.72699 11950.722
		620 283.40879 -3160.5911 -2739.042 455.28104 11950.775
		630 292.53718 -3166.3125 -2731.1856 296.63465 11950.838
		640 302.81112 -3173.3096 -2722.901 113.80844 11950.907
		650 309.83321 -3179.3684 -2718.515 -26.499431 11950.978
		660 312.1283 -3182.7335 -2718.4663 -89.363745 11951.049
		670 311.16363 -3181.867 -2719.0347 -69.370989 11951.118
		680 308.51041 -3180.6869 -2721.801 -25.972987 11951.186
		690 304.64393 -3176.8751 -2723.7403 56.592367 11951.254
		700 300.24456 -3175.4797 -2728.8887 112.34442 11951.323
		710 296.35785 -3172.9705 -2732.1607 168.18009 11951.394
		720 293.78145 -3172.1065 -2735.1289 182.81082 11951.468
		730 293.25707 -3170.8715 -2734.6738 171.04236 11951.547
		740 295.33219 -3172.9109 -2733.6266 91.351362 11951.629
		750 299.69136 -3175.2574 -2729.4892 -16.266404 11951.713
		760 305.2281 -3177.9836 -2723.9799 -137.30615 11951.796
		770 310.59309 -3182.7053 -2720.7216 -272.72961 11951.877
		780 314.65573 -3183.4212 -2715.3947 -341.231 11951.952
		790 316.48606 -3185.44 -2714.691 -388.53602 11952.02
		800 315.15897 -3186.846 -2718.0709 -384.28316 11952.08
		810 310.43559 -3183.6648 -2721.9154 -282.61999 11952.133
		820 303.22265 -3178.464 -2727.4433 -121.47565 11952.179
		830 295.36843 -3175.4771 -2736.1389 33.066504 11952.223
		840 288.69698 -3169.5813 -2740.1664 216.10697 11952.268
		850 283.82649 -3165.7822 -2743.6118 359.56896 11952.317
		860 280.04102 -3162.8228 -2746.283 475.61942 11952.374
		870 277.10059 -3159.6212 -2747.4551 572.5432 11952.441
		880 275.76549 -3158.2545 -2748.0743 616.43304 11952.52
		890 276.82327 -3158.9703 -2747.2166 596.08147 11952.612
		900 280.72135 -3162.0637 -2744.5119 506.33695 11952.716
		910 287.1035 -3167.4388 -2740.3941 356.68688 11952.831
		920 294.28041 -3171.6218 -2733.902 206.06394 11952.953
		930 300.36009 -3173.9046 -2727.1418 88.047911 11953.08
		940 303.86761 -3175.5599 -2723.5798 7.6846808 11953.209
		950 304.42957 -3176.0831 -2723.2672 -25.15496 11953.339
		960 303.13982 -3176.0534 -2725.1559 -28.715178 11953.467
		970 302.30166 -3176.9758 -2727.325 -43.264668 11953.596
		980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
		990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
		1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
		Loop time of 0.248474 on 1 procs for 1000 steps with 500 atoms

		Performance: 347.722 ns/day, 0.069 hours/ns, 4024.566 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 \| 0.20529 \| 0.20529 \| 0.20529 \| 0.0 \| 82.62
		Bond \| 8.4e-05 \| 8.4e-05 \| 8.4e-05 \| 0.0 \| 0.03
		Neigh \| 0.004163 \| 0.004163 \| 0.004163 \| 0.0 \| 1.68
		Comm \| 0.007817 \| 0.007817 \| 0.007817 \| 0.0 \| 3.15
		Output \| 0.001142 \| 0.001142 \| 0.001142 \| 0.0 \| 0.46
		Modify \| 0.026383 \| 0.026383 \| 0.026383 \| 0.0 \| 10.62
		Other \| \| 0.003598 \| \| \| 1.45

		Nlocal: 500 ave 500 max 500 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 1610 ave 1610 max 1610 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 14765 ave 14765 max 14765 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 14765
		Ave neighs/atom = 29.53
		Ave special neighs/atom = 0
		Neighbor list builds = 5
		Dangerous builds = 0

		#write_data lj-out.data
		Total wall time: 0:00:00

examples/USER/misc/grem/lj-single/log.gREM.9Nov16.g++.4

0 → 100644

+180 −0

Original line number	Diff line number	Diff line
		LAMMPS (9 Nov 2016)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
		using 1 OpenMP thread(s) per MPI task
		# LJ particles
		variable T0 equal 300.0
		variable press equal 0.0

		units real
		atom_style full
		pair_style lj/cut 5.0

		read_data "lj.data"
		orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
		1 by 2 by 2 MPI processor grid
		reading atoms ...
		500 atoms
		reading velocities ...
		500 velocities
		0 = max # of 1-2 neighbors
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors

		thermo 10
		thermo_style custom step temp pe etotal press vol

		timestep 1.0

		fix fxgREM all grem 400 -.01 -30000 ${T0} ${press}
		fix fxgREM all grem 400 -.01 -30000 300 ${press}
		fix fxgREM all grem 400 -.01 -30000 300 0
		fix fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
		fix fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
		thermo_modify press fxgREM_press
		fix_modify fxnvt press fxgREM_press
		run 1000
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 7
		ghost atom cutoff = 7
		binsize = 3.5 -> bins = 7 7 7
		Memory usage per processor = 5.34276 Mbytes
		Step Temp PotEng TotEng Press Volume
		0 305.69499 -3177.6423 -2722.9442 -91.741776 11950.115
		10 312.30124 -3182.2257 -2717.7013 -203.95075 11950.113
		20 314.94567 -3186.456 -2717.9982 -265.56737 11950.108
		30 312.229 -3183.7641 -2719.3472 -196.90499 11950.097
		40 305.94068 -3180.7085 -2725.6449 -92.562221 11950.083
		50 300.42281 -3176.5838 -2729.7277 10.896769 11950.066
		60 299.16747 -3174.1939 -2729.205 50.094171 11950.05
		70 301.65965 -3176.0918 -2727.396 0.096901939 11950.035
		80 304.77876 -3178.2699 -2724.9346 -64.001022 11950.019
		90 305.60598 -3178.9517 -2724.386 -93.672879 11950.003
		100 303.8005 -3177.5156 -2725.6354 -74.516709 11949.985
		110 300.86776 -3175.4773 -2727.9593 -34.22655 11949.965
		120 298.70177 -3175.6488 -2731.3526 -19.014898 11949.944
		130 298.39686 -3176.3792 -2732.5365 -21.293245 11949.923
		140 300.00669 -3177.7032 -2731.466 -40.992937 11949.902
		150 301.85665 -3178.1312 -2729.1423 -45.715505 11949.88
		160 301.20597 -3177.3218 -2729.3007 -10.104082 11949.857
		170 297.01134 -3172.7462 -2730.9643 99.298381 11949.833
		180 291.279 -3168.3513 -2735.0958 219.47549 11949.812
		190 287.13954 -3165.1287 -2738.0304 309.36947 11949.796
		200 286.57735 -3165.2951 -2739.033 323.96954 11949.786
		210 289.83941 -3167.8245 -2736.7103 271.77305 11949.783
		220 296.12858 -3171.8054 -2731.3366 172.4056 11949.785
		230 303.82424 -3176.3108 -2724.3952 56.711479 11949.791
		240 309.95738 -3180.9789 -2719.9408 -40.992898 11949.798
		250 312.0405 -3182.3473 -2718.2107 -57.591676 11949.805
		260 309.65444 -3181.0587 -2720.4712 3.3540332 11949.81
		270 304.40001 -3176.5798 -2723.8078 130.77028 11949.816
		280 298.65985 -3174.1505 -2729.9166 237.63562 11949.825
		290 294.78709 -3170.9701 -2732.4966 326.94924 11949.838
		300 294.03216 -3169.9567 -2732.6062 349.85486 11949.859
		310 296.44397 -3172.8519 -2731.914 284.80897 11949.886
		320 301.41027 -3175.9697 -2727.6447 179.4647 11949.92
		330 307.88911 -3181.2615 -2723.2998 24.702414 11949.957
		340 314.73138 -3186.0047 -2717.8656 -132.6263 11949.995
		350 320.55591 -3187.8509 -2711.0483 -245.88468 11950.031
		360 323.50274 -3188.9994 -2707.8136 -314.73676 11950.062
		370 321.61539 -3187.1233 -2708.7448 -293.17446 11950.086
		380 314.37275 -3181.484 -2713.8784 -169.00448 11950.104
		390 303.54884 -3174.1675 -2722.6616 12.923999 11950.119
		400 293.40432 -3167.0348 -2730.6181 187.6624 11950.135
		410 288.46351 -3165.273 -2736.2054 252.20051 11950.154
		420 290.31387 -3168.604 -2736.7841 193.73816 11950.178
		430 296.35519 -3173.09 -2732.2841 81.521847 11950.207
		440 301.92973 -3175.4344 -2726.3368 -1.8329439 11950.237
		450 303.76205 -3176.777 -2724.9539 -35.002096 11950.267
		460 301.71619 -3174.2731 -2725.4932 14.977875 11950.296
		470 298.92404 -3172.9921 -2728.3652 64.224747 11950.326
		480 298.80164 -3172.5329 -2728.0881 82.781347 11950.358
		490 302.71589 -3175.3703 -2725.1034 27.223049 11950.39
		500 309.10665 -3179.3013 -2719.5285 -65.460658 11950.424
		510 314.36408 -3183.2854 -2715.6927 -151.19245 11950.456
		520 315.71154 -3183.5328 -2713.9358 -163.19151 11950.485
		530 313.31886 -3182.2521 -2716.214 -125.5741 11950.511
		540 309.81847 -3178.9358 -2718.1043 -55.55841 11950.534
		550 308.29687 -3177.837 -2719.2688 -24.39371 11950.556
		560 308.75927 -3176.3265 -2717.0705 0.93689833 11950.578
		570 307.52811 -3175.8145 -2718.3897 35.502429 11950.6
		580 301.75074 -3173.1208 -2724.2894 136.29625 11950.622
		590 292.37743 -3165.5806 -2730.6913 319.75957 11950.648
		600 283.57627 -3159.8617 -2738.0635 471.28045 11950.68
		610 279.85172 -3157.4557 -2741.1975 530.72699 11950.722
		620 283.40879 -3160.5911 -2739.042 455.28104 11950.775
		630 292.53718 -3166.3125 -2731.1856 296.63465 11950.838
		640 302.81112 -3173.3096 -2722.901 113.80844 11950.907
		650 309.83321 -3179.3684 -2718.515 -26.499431 11950.978
		660 312.1283 -3182.7335 -2718.4663 -89.363745 11951.049
		670 311.16363 -3181.867 -2719.0347 -69.370989 11951.118
		680 308.51041 -3180.6869 -2721.801 -25.972987 11951.186
		690 304.64393 -3176.8751 -2723.7403 56.592367 11951.254
		700 300.24456 -3175.4797 -2728.8887 112.34442 11951.323
		710 296.35785 -3172.9705 -2732.1607 168.18009 11951.394
		720 293.78145 -3172.1065 -2735.1289 182.81082 11951.468
		730 293.25707 -3170.8715 -2734.6738 171.04236 11951.547
		740 295.33219 -3172.9109 -2733.6266 91.351362 11951.629
		750 299.69136 -3175.2574 -2729.4892 -16.266404 11951.713
		760 305.2281 -3177.9836 -2723.9799 -137.30615 11951.796
		770 310.59309 -3182.7053 -2720.7216 -272.72961 11951.877
		780 314.65573 -3183.4212 -2715.3947 -341.231 11951.952
		790 316.48606 -3185.44 -2714.691 -388.53602 11952.02
		800 315.15897 -3186.846 -2718.0709 -384.28316 11952.08
		810 310.43559 -3183.6648 -2721.9154 -282.61999 11952.133
		820 303.22265 -3178.464 -2727.4433 -121.47565 11952.179
		830 295.36843 -3175.4771 -2736.1389 33.066504 11952.223
		840 288.69698 -3169.5813 -2740.1664 216.10697 11952.268
		850 283.82649 -3165.7822 -2743.6118 359.56896 11952.317
		860 280.04102 -3162.8228 -2746.283 475.61942 11952.374
		870 277.10059 -3159.6212 -2747.4551 572.5432 11952.441
		880 275.76549 -3158.2545 -2748.0743 616.43304 11952.52
		890 276.82327 -3158.9703 -2747.2166 596.08147 11952.612
		900 280.72135 -3162.0637 -2744.5119 506.33695 11952.716
		910 287.1035 -3167.4388 -2740.3941 356.68688 11952.831
		920 294.28041 -3171.6218 -2733.902 206.06394 11952.953
		930 300.36009 -3173.9046 -2727.1418 88.047911 11953.08
		940 303.86761 -3175.5599 -2723.5798 7.6846808 11953.209
		950 304.42957 -3176.0831 -2723.2672 -25.15496 11953.339
		960 303.13982 -3176.0534 -2725.1559 -28.715178 11953.467
		970 302.30166 -3176.9758 -2727.325 -43.264668 11953.596
		980 303.93331 -3178.9891 -2726.9114 -88.434034 11953.723
		990 307.36223 -3180.7316 -2723.5535 -145.46208 11953.849
		1000 310.09574 -3181.101 -2719.8571 -180.39125 11953.972
		Loop time of 0.203733 on 4 procs for 1000 steps with 500 atoms

		Performance: 424.084 ns/day, 0.057 hours/ns, 4908.379 timesteps/s
		84.1% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.09278 \| 0.097682 \| 0.10458 \| 1.4 \| 47.95
		Bond \| 8.1e-05 \| 0.00010075 \| 0.000116 \| 0.1 \| 0.05
		Neigh \| 0.001528 \| 0.001553 \| 0.00159 \| 0.1 \| 0.76
		Comm \| 0.03798 \| 0.045863 \| 0.050976 \| 2.4 \| 22.51
		Output \| 0.001655 \| 0.0066915 \| 0.021705 \| 10.6 \| 3.28
		Modify \| 0.033916 \| 0.047091 \| 0.053775 \| 3.7 \| 23.11
		Other \| \| 0.004751 \| \| \| 2.33

		Nlocal: 125 ave 127 max 123 min
		Histogram: 1 0 1 0 0 0 0 1 0 1
		Nghost: 870.5 ave 882 max 862 min
		Histogram: 1 1 0 0 0 0 1 0 0 1
		Neighs: 3691.25 ave 3807 max 3563 min
		Histogram: 1 0 0 0 1 0 1 0 0 1

		Total # of neighbors = 14765
		Ave neighs/atom = 29.53
		Ave special neighs/atom = 0
		Neighbor list builds = 5
		Dangerous builds = 0

		#write_data lj-out.data
		Total wall time: 0:00:00

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