update log files for kolmogorov/crespi/full potential (e9666f58) · Commits · 郑智淋 / lammps

examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.1→examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.1

+27 −24

Original line number	Diff line number	Diff line
		LAMMPS (8 Mar 2018)
		LAMMPS (5 Jun 2019)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
		using 1 OpenMP thread(s) per MPI task
		# Initialization
		units metal
		@@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors
		special bonds CPU = 0.000353813 secs
		read_data CPU = 0.0043292 secs
		mass 1 12.0107 # carbon mass (g/mole) \| membrane
		mass 2 12.0107 # carbon mass (g/mole) \| adsorbate
		# Separate atom groups
		@@ -32,8 +35,8 @@ group adsorbate type 2
		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
		####################################################################
		pair_coeff * * rebo CH.airebo NULL C # chemical
		Reading potential file CH.airebo with DATE: 2011-10-25
		pair_coeff * * rebo CH.rebo NULL C # chemical
		Reading potential file CH.rebo with DATE: 2018-7-3
		pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
		####################################################################
		# Neighbor update settings
		@@ -92,32 +95,32 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 16.96 \| 16.96 \| 16.96 Mbytes
		Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
		0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
		100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
		200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
		300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
		400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
		500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
		600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
		700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
		800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
		900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
		1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
		Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms
		0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
		100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
		200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
		300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
		400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
		500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
		600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
		700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
		800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
		900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
		1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
		Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms

		Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
		Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 timesteps/s
		99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 155.99 \| 155.99 \| 155.99 \| 0.0 \| 99.90
		Bond \| 0.00075769 \| 0.00075769 \| 0.00075769 \| 0.0 \| 0.00
		Pair \| 103.59 \| 103.59 \| 103.59 \| 0.0 \| 99.87
		Bond \| 0.00022388 \| 0.00022388 \| 0.00022388 \| 0.0 \| 0.00
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.084217 \| 0.084217 \| 0.084217 \| 0.0 \| 0.05
		Output \| 0.0016122 \| 0.0016122 \| 0.0016122 \| 0.0 \| 0.00
		Modify \| 0.034797 \| 0.034797 \| 0.034797 \| 0.0 \| 0.02
		Other \| \| 0.02838 \| \| \| 0.02
		Comm \| 0.082476 \| 0.082476 \| 0.082476 \| 0.0 \| 0.08
		Output \| 0.0010884 \| 0.0010884 \| 0.0010884 \| 0.0 \| 0.00
		Modify \| 0.032938 \| 0.032938 \| 0.032938 \| 0.0 \| 0.03
		Other \| \| 0.01749 \| \| \| 0.02

		Nlocal: 1360 ave 1360 max 1360 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
		Ave special neighs/atom = 0
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:02:36
		Total wall time: 0:01:43

examples/USER/misc/kolmogorov_crespi_full/log.16Mar18.bilayer-graphene.g++.4→examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.g++.4

+27 −24

Original line number	Diff line number	Diff line
		LAMMPS (8 Mar 2018)
		LAMMPS (5 Jun 2019)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
		using 1 OpenMP thread(s) per MPI task
		# Initialization
		units metal
		@@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors
		special bonds CPU = 0.000187874 secs
		read_data CPU = 0.00234103 secs
		mass 1 12.0107 # carbon mass (g/mole) \| membrane
		mass 2 12.0107 # carbon mass (g/mole) \| adsorbate
		# Separate atom groups
		@@ -32,8 +35,8 @@ group adsorbate type 2
		######################## Potential defition ########################
		pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
		####################################################################
		pair_coeff * * rebo CH.airebo NULL C # chemical
		Reading potential file CH.airebo with DATE: 2011-10-25
		pair_coeff * * rebo CH.rebo NULL C # chemical
		Reading potential file CH.rebo with DATE: 2018-7-3
		pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
		####################################################################
		# Neighbor update settings
		@@ -92,32 +95,32 @@ Neighbor list info ...
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 11.13 \| 11.13 \| 11.13 Mbytes
		Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
		0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
		100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
		200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
		300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
		400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
		500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
		600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
		700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
		800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
		900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
		1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
		Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms
		0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
		100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
		200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
		300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
		400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
		500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
		600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
		700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
		800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
		900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
		1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
		Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms

		Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s
		98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
		Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s
		94.1% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 39.928 \| 40.992 \| 42.377 \| 15.8 \| 96.36
		Bond \| 0.0003643 \| 0.00043392 \| 0.00048113 \| 0.0 \| 0.00
		Pair \| 30.833 \| 31.356 \| 32.18 \| 9.1 \| 92.95
		Bond \| 0.00026059 \| 0.00029182 \| 0.00031185 \| 0.0 \| 0.00
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.12253 \| 1.5076 \| 2.5698 \| 82.1 \| 3.54
		Output \| 0.0012577 \| 0.0013637 \| 0.0016453 \| 0.4 \| 0.00
		Modify \| 0.010833 \| 0.012247 \| 0.013317 \| 0.9 \| 0.03
		Other \| \| 0.02864 \| \| \| 0.07
		Comm \| 1.443 \| 2.2722 \| 2.8091 \| 34.3 \| 6.74
		Output \| 0.00068855 \| 0.00095087 \| 0.0017185 \| 0.0 \| 0.00
		Modify \| 0.010187 \| 0.011709 \| 0.015284 \| 1.9 \| 0.03
		Other \| \| 0.09241 \| \| \| 0.27

		Nlocal: 340 ave 344 max 334 min
		Histogram: 1 0 0 0 0 0 1 0 1 1
		@@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
		Ave special neighs/atom = 0
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:00:42
		Total wall time: 0:00:33

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