update log files for coreshell examples (98c8f220) · Commits · 郑智淋 / lammps

examples/coreshell/log.9Nov16.coreshell.dsf.g++.1→examples/coreshell/log.27Nov18.coreshell.dsf.g++.1

+32 −26

Changes for examples/coreshell/log.27Nov18.coreshell.dsf.g++.1: 32 added lines, 26 removed lines.
Original line number	Diff line number	Diff line
		LAMMPS (27 Oct 2016)
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Hendrik Heenen, June 2014

		@@ -68,12 +69,17 @@ thermo_modify temp CSequ

		velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
		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 = 22
		ghost atom cutoff = 22
		binsize = 11 -> bins = 3 3 3
		binsize = 11, bins = 3 3 3
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair born/coul/dsf/cs, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		velocity all scale 1427 temp CSequ

		fix thermoberendsen all temp/berendsen 1427 1427 0.4
		@@ -84,7 +90,7 @@ fix_modify thermoberendsen temp CSequ

		timestep 0.002
		run 500
		Memory usage per processor = 7.04355 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 8.59 \| 8.59 \| 8.59 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.3517686e-14 2.942091e-15 13990.5
		50 -633.9898 -666.02679 32.03699 1152.7858 -4578.5681 -668.50431 37.800204 -706.30452 0 2.4775226 14.568073 4.3012389 13990.5
		@@ -97,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
		400 -625.02586 -661.46042 36.434568 1311.0236 -868.2031 -664.40231 43.21398 -707.61629 0 2.9418875 14.945389 2.7493413 13990.5
		450 -624.3278 -660.50844 36.180639 1301.8865 -2203.3944 -663.49896 40.008669 -703.50763 0 2.9905179 14.158866 1.7299899 13990.5
		500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
		Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms
		Loop time of 8.43387 on 1 procs for 500 steps with 432 atoms

		Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s
		99.9% CPU use with 1 MPI tasks x no OpenMP threads
		Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 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 \| 10.478 \| 10.478 \| 10.478 \| 0.0 \| 97.78
		Bond \| 0.0029511 \| 0.0029511 \| 0.0029511 \| 0.0 \| 0.03
		Neigh \| 0.14159 \| 0.14159 \| 0.14159 \| 0.0 \| 1.32
		Comm \| 0.074382 \| 0.074382 \| 0.074382 \| 0.0 \| 0.69
		Output \| 0.00054097 \| 0.00054097 \| 0.00054097 \| 0.0 \| 0.01
		Modify \| 0.010588 \| 0.010588 \| 0.010588 \| 0.0 \| 0.10
		Other \| \| 0.007748 \| \| \| 0.07
		Pair \| 8.1175 \| 8.1175 \| 8.1175 \| 0.0 \| 96.25
		Bond \| 0.0019796 \| 0.0019796 \| 0.0019796 \| 0.0 \| 0.02
		Neigh \| 0.21242 \| 0.21242 \| 0.21242 \| 0.0 \| 2.52
		Comm \| 0.085533 \| 0.085533 \| 0.085533 \| 0.0 \| 1.01
		Output \| 0.00041103 \| 0.00041103 \| 0.00041103 \| 0.0 \| 0.00
		Modify \| 0.012187 \| 0.012187 \| 0.012187 \| 0.0 \| 0.14
		Other \| \| 0.003863 \| \| \| 0.05

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -131,7 +137,7 @@ unfix thermoberendsen
		# ------------------------ Dynamic Run -------------------------------

		run 1000
		Memory usage per processor = 7.04355 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 8.59 \| 8.59 \| 8.59 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
		550 -623.5004 -660.74472 37.244326 1340.1611 -1413.4326 -663.99669 41.875014 -705.8717 0 3.2519651 15.097948 2.278405 13990.5
		@@ -154,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
		1400 -623.50803 -660.03912 36.53109 1314.4968 362.97431 -663.24909 45.772904 -709.02199 0 3.2099708 14.566488 1.9170714 13990.5
		1450 -623.51243 -659.65548 36.143052 1300.534 2853.0755 -663.0534 51.355353 -714.40875 0 3.3979157 15.890282 2.5251359 13990.5
		1500 -623.51621 -661.87741 38.361201 1380.3496 740.04973 -665.00896 46.208742 -711.2177 0 3.1315492 15.168927 2.4710846 13990.5
		Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms
		Loop time of 16.907 on 1 procs for 1000 steps with 432 atoms

		Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s
		99.9% CPU use with 1 MPI tasks x no OpenMP threads
		Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 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 \| 21.8 \| 21.8 \| 21.8 \| 0.0 \| 97.86
		Bond \| 0.005852 \| 0.005852 \| 0.005852 \| 0.0 \| 0.03
		Neigh \| 0.30423 \| 0.30423 \| 0.30423 \| 0.0 \| 1.37
		Comm \| 0.14388 \| 0.14388 \| 0.14388 \| 0.0 \| 0.65
		Output \| 0.0010855 \| 0.0010855 \| 0.0010855 \| 0.0 \| 0.00
		Modify \| 0.0064189 \| 0.0064189 \| 0.0064189 \| 0.0 \| 0.03
		Other \| \| 0.01527 \| \| \| 0.07
		Pair \| 16.247 \| 16.247 \| 16.247 \| 0.0 \| 96.09
		Bond \| 0.0039518 \| 0.0039518 \| 0.0039518 \| 0.0 \| 0.02
		Neigh \| 0.46795 \| 0.46795 \| 0.46795 \| 0.0 \| 2.77
		Comm \| 0.17146 \| 0.17146 \| 0.17146 \| 0.0 \| 1.01
		Output \| 0.00082397 \| 0.00082397 \| 0.00082397 \| 0.0 \| 0.00
		Modify \| 0.0065799 \| 0.0065799 \| 0.0065799 \| 0.0 \| 0.04
		Other \| \| 0.009467 \| \| \| 0.06

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -182,4 +188,4 @@ Ave neighs/atom = 687.803
		Ave special neighs/atom = 1
		Neighbor list builds = 44
		Dangerous builds = 0
		Total wall time: 0:00:33
		Total wall time: 0:00:25

examples/coreshell/log.9Nov16.coreshell.dsf.g++.4→examples/coreshell/log.27Nov18.coreshell.dsf.g++.4

+27 −25

Changes for examples/coreshell/log.27Nov18.coreshell.dsf.g++.4: 27 added lines, 25 removed lines.
Original line number	Diff line number	Diff line
		LAMMPS (26 Jan 2017)
		LAMMPS (27 Nov 2018)
		using 1 OpenMP thread(s) per MPI task
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Hendrik Heenen, June 2014

		@@ -74,7 +75,8 @@ Neighbor list info ...
		ghost atom cutoff = 22
		binsize = 11, bins = 3 3 3
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair born/coul/dsf/cs, half, perpetual
		(1) pair born/coul/dsf/cs, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		@@ -88,7 +90,7 @@ fix_modify thermoberendsen temp CSequ

		timestep 0.002
		run 500
		Memory usage per processor = 6.8559 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 6.881 \| 6.881 \| 6.881 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.5814015e-14 3.2317898e-15 13990.5
		50 -634.07021 -666.11867 32.048452 1153.1982 -4560.945 -668.28236 37.756542 -706.0389 0 2.163691 13.802484 3.022372 13990.5
		@@ -101,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
		400 -625.09344 -661.26404 36.1706 1301.5253 -729.96729 -664.10334 43.468765 -707.57211 0 2.8392963 13.663555 1.9067551 13990.5
		450 -624.46214 -660.01362 35.551477 1279.2474 -1617.7158 -663.06571 41.644856 -704.71057 0 3.0520921 14.527005 1.7280213 13990.5
		500 -623.49246 -659.2527 35.76024 1286.7593 -935.99238 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
		Loop time of 4.09864 on 4 procs for 500 steps with 432 atoms
		Loop time of 2.44013 on 4 procs for 500 steps with 432 atoms

		Performance: 21.080 ns/day, 1.139 hours/ns, 121.992 timesteps/s
		99.7% CPU use with 4 MPI tasks x no OpenMP threads
		Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s
		98.6% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 3.3804 \| 3.568 \| 3.8354 \| 8.9 \| 87.05
		Bond \| 0.00074339 \| 0.00079519 \| 0.00087976 \| 0.0 \| 0.02
		Neigh \| 0.045851 \| 0.046084 \| 0.046361 \| 0.1 \| 1.12
		Comm \| 0.20413 \| 0.47123 \| 0.65875 \| 24.3 \| 11.50
		Output \| 0.00044298 \| 0.00046057 \| 0.00051165 \| 0.0 \| 0.01
		Modify \| 0.0064909 \| 0.0067219 \| 0.0069766 \| 0.2 \| 0.16
		Other \| \| 0.005345 \| \| \| 0.13
		Pair \| 2.0321 \| 2.1124 \| 2.1759 \| 3.6 \| 86.57
		Bond \| 0.00069523 \| 0.00071579 \| 0.00074148 \| 0.0 \| 0.03
		Neigh \| 0.060491 \| 0.060606 \| 0.060709 \| 0.0 \| 2.48
		Comm \| 0.19263 \| 0.25562 \| 0.33556 \| 10.4 \| 10.48
		Output \| 0.00041246 \| 0.00057316 \| 0.0010512 \| 0.0 \| 0.02
		Modify \| 0.0059495 \| 0.0062472 \| 0.006577 \| 0.4 \| 0.26
		Other \| \| 0.00394 \| \| \| 0.16

		Nlocal: 108 ave 114 max 105 min
		Histogram: 1 1 1 0 0 0 0 0 0 1
		@@ -135,7 +137,7 @@ unfix thermoberendsen
		# ------------------------ Dynamic Run -------------------------------

		run 1000
		Memory usage per processor = 6.85787 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 6.883 \| 6.948 \| 7.138 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		500 -623.49319 -659.2527 35.759511 1286.7331 -936.04802 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
		550 -623.44059 -663.57938 40.138795 1444.3127 -935.73484 -666.2789 42.563337 -708.84224 0 2.6995167 13.918509 2.3189805 13990.5
		@@ -158,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm
		1400 -623.47124 -661.45375 37.982513 1366.7233 -379.56023 -664.6321 43.788306 -708.42041 0 3.1783497 14.251126 1.7415409 13990.5
		1450 -623.46671 -660.17518 36.708464 1320.8792 -374.37056 -662.92706 44.083648 -707.01071 0 2.7518803 15.210167 1.9984277 13990.5
		1500 -623.50515 -659.06488 35.559725 1279.5442 260.37822 -662.39548 45.779764 -708.17524 0 3.3306005 14.682396 2.4201107 13990.5
		Loop time of 8.26746 on 4 procs for 1000 steps with 432 atoms
		Loop time of 5.16152 on 4 procs for 1000 steps with 432 atoms

		Performance: 20.901 ns/day, 1.148 hours/ns, 120.956 timesteps/s
		99.7% CPU use with 4 MPI tasks x no OpenMP threads
		Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s
		98.3% CPU use with 4 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 6.706 \| 7.1568 \| 7.6597 \| 12.7 \| 86.57
		Bond \| 0.0014617 \| 0.0015531 \| 0.0016506 \| 0.2 \| 0.02
		Neigh \| 0.10511 \| 0.10522 \| 0.10532 \| 0.0 \| 1.27
		Comm \| 0.48547 \| 0.98841 \| 1.4393 \| 34.0 \| 11.96
		Output \| 0.0012085 \| 0.0012462 \| 0.0013196 \| 0.1 \| 0.02
		Modify \| 0.0021446 \| 0.0021989 \| 0.0022545 \| 0.1 \| 0.03
		Other \| \| 0.01204 \| \| \| 0.15
		Pair \| 4.0761 \| 4.2795 \| 4.6259 \| 10.9 \| 82.91
		Bond \| 0.0013907 \| 0.0014481 \| 0.0015037 \| 0.1 \| 0.03
		Neigh \| 0.13612 \| 0.13618 \| 0.13624 \| 0.0 \| 2.64
		Comm \| 0.38391 \| 0.73074 \| 0.93346 \| 26.3 \| 14.16
		Output \| 0.00096703 \| 0.0014517 \| 0.0028937 \| 2.2 \| 0.03
		Modify \| 0.0022988 \| 0.0024452 \| 0.0025537 \| 0.2 \| 0.05
		Other \| \| 0.009786 \| \| \| 0.19

		Nlocal: 108 ave 114 max 94 min
		Histogram: 1 0 0 0 0 0 0 0 1 2
		@@ -186,4 +188,4 @@ Ave neighs/atom = 687.484
		Ave special neighs/atom = 1
		Neighbor list builds = 46
		Dangerous builds = 0
		Total wall time: 0:00:12
		Total wall time: 0:00:07

examples/coreshell/log.5Oct16.coreshell.g++.1→examples/coreshell/log.27Nov18.coreshell.g++.1

+83 −74

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examples/coreshell/log.5Oct16.coreshell.g++.4→examples/coreshell/log.27Nov18.coreshell.g++.4

+89 −80

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examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1

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