change input and log files for new example to give consistent results in serial and parallel. (b97cd78e) · Commits · 郑智淋 / lammps

examples/snap/in.snap.InP.JCPA2020

+1 −1

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ neigh_modify once no every 1 delay 0 check yes

		# Run MD

		velocity all create 300.0 4928459
		velocity all create 300.0 4928459 loop geom
		fix 1 all nve
		run ${nsteps}

examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1→examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.1

+27 −26

Original line number	Diff line number	Diff line
		LAMMPS (2 Jun 2020)
		LAMMPS (15 Jun 2020)
		using 1 OpenMP thread(s) per MPI task
		# Demonstrate SNAP InP potential

		# Initialize simulation
		@@ -43,10 +44,10 @@ include InP_JCPA2020.snap

		# Definition of SNAP+ZBL potential.

		variable zblcutinner equal 4
		variable zblcutouter equal 4.2
		variable zblz1 equal 49
		variable zblz2 equal 15
		variable zblcutinner index 4
		variable zblcutouter index 4.2
		variable zblz1 index 49
		variable zblz2 index 15

		# Specify hybrid with SNAP and ZBL

		@@ -90,7 +91,7 @@ neigh_modify once no every 1 delay 0 check yes

		# Run MD

		velocity all create 300.0 4928459
		velocity all create 300.0 4928459 loop geom
		fix 1 all nve
		run ${nsteps}
		run 100
		@@ -114,30 +115,30 @@ Neighbor list info ...
		Per MPI rank memory allocation (min/avg/max) = 6.027 \| 6.027 \| 6.027 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 300 -3.4805794 0 -3.4418771 1353.5968
		10 286.42264 -3.4788274 0 -3.4418767 1586.4881
		20 250.14148 -3.4741459 0 -3.4418757 2219.0344
		30 202.52417 -3.4680017 0 -3.4418745 2982.7272
		40 157.39113 -3.4621782 0 -3.4418735 3631.0936
		50 126.7004 -3.4582183 0 -3.441873 4053.7725
		60 117.00722 -3.4569679 0 -3.441873 4204.9542
		70 127.65968 -3.4583427 0 -3.4418736 4106.3112
		80 151.50217 -3.4614195 0 -3.4418745 3840.7205
		90 177.67607 -3.464797 0 -3.4418754 3527.9794
		100 195.30359 -3.4670717 0 -3.4418761 3300.3795
		Loop time of 18.0803 on 1 procs for 100 steps with 512 atoms

		Performance: 0.239 ns/day, 100.446 hours/ns, 5.531 timesteps/s
		99.8% CPU use with 1 MPI tasks x no OpenMP threads
		10 285.84677 -3.4787531 0 -3.4418766 1611.7131
		20 248.14649 -3.4738884 0 -3.4418756 2312.0308
		30 198.94136 -3.4675394 0 -3.4418744 3168.1543
		40 152.74831 -3.4615791 0 -3.4418734 3903.5749
		50 121.9796 -3.4576091 0 -3.4418728 4387.1254
		60 113.27555 -3.4564863 0 -3.4418729 4556.3003
		70 125.68089 -3.4580873 0 -3.4418735 4431.2083
		80 151.47475 -3.4614159 0 -3.4418745 4107.2369
		90 179.18708 -3.4649919 0 -3.4418754 3739.5881
		100 197.50662 -3.4673559 0 -3.441876 3492.7778
		Loop time of 13.3103 on 1 procs for 100 steps with 512 atoms

		Performance: 0.325 ns/day, 73.946 hours/ns, 7.513 timesteps/s
		99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 18.078 \| 18.078 \| 18.078 \| 0.0 \| 99.99
		Pair \| 13.309 \| 13.309 \| 13.309 \| 0.0 \| 99.99
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.000979 \| 0.000979 \| 0.000979 \| 0.0 \| 0.01
		Output \| 0.000243 \| 0.000243 \| 0.000243 \| 0.0 \| 0.00
		Modify \| 0.000591 \| 0.000591 \| 0.000591 \| 0.0 \| 0.00
		Other \| \| 0.000469 \| \| \| 0.00
		Comm \| 0.00068474 \| 0.00068474 \| 0.00068474 \| 0.0 \| 0.01
		Output \| 0.00020504 \| 0.00020504 \| 0.00020504 \| 0.0 \| 0.00
		Modify \| 0.0003829 \| 0.0003829 \| 0.0003829 \| 0.0 \| 0.00
		Other \| \| 0.0004075 \| \| \| 0.00

		Nlocal: 512 ave 512 max 512 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		@@ -153,4 +154,4 @@ Ave neighs/atom = 122
		Neighbor list builds = 0
		Dangerous builds = 0

		Total wall time: 0:00:18
		Total wall time: 0:00:13

examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4→examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.4

+28 −27

Original line number	Diff line number	Diff line
		LAMMPS (2 Jun 2020)
		LAMMPS (15 Jun 2020)
		using 1 OpenMP thread(s) per MPI task
		# Demonstrate SNAP InP potential

		# Initialize simulation
		@@ -31,7 +32,7 @@ Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
		1 by 2 by 2 MPI processor grid
		create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
		Created 512 atoms
		create_atoms CPU = 0.001 seconds
		create_atoms CPU = 0.000 seconds

		mass 1 114.76
		mass 2 30.98
		@@ -43,10 +44,10 @@ include InP_JCPA2020.snap

		# Definition of SNAP+ZBL potential.

		variable zblcutinner equal 4
		variable zblcutouter equal 4.2
		variable zblz1 equal 49
		variable zblz2 equal 15
		variable zblcutinner index 4
		variable zblcutouter index 4.2
		variable zblz1 index 49
		variable zblz2 index 15

		# Specify hybrid with SNAP and ZBL

		@@ -90,7 +91,7 @@ neigh_modify once no every 1 delay 0 check yes

		# Run MD

		velocity all create 300.0 4928459
		velocity all create 300.0 4928459 loop geom
		fix 1 all nve
		run ${nsteps}
		run 100
		@@ -114,30 +115,30 @@ Neighbor list info ...
		Per MPI rank memory allocation (min/avg/max) = 4.587 \| 4.587 \| 4.587 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 300 -3.4805794 0 -3.4418771 1353.5968
		10 286.58246 -3.478848 0 -3.4418767 1582.995
		20 250.70996 -3.4742192 0 -3.4418757 2207.7507
		30 203.58199 -3.4681382 0 -3.4418746 2968.5206
		40 158.84622 -3.462366 0 -3.4418736 3619.0285
		50 128.30488 -3.4584254 0 -3.4418731 4047.173
		60 118.40349 -3.4571481 0 -3.4418731 4203.3421
		70 128.48973 -3.4584499 0 -3.4418737 4109.0296
		80 151.54241 -3.4614247 0 -3.4418746 3847.4617
		90 176.92084 -3.4646996 0 -3.4418755 3548.7811
		100 193.9555 -3.4668978 0 -3.4418761 3342.8083
		Loop time of 4.99339 on 4 procs for 100 steps with 512 atoms

		Performance: 0.865 ns/day, 27.741 hours/ns, 20.026 timesteps/s
		99.5% CPU use with 4 MPI tasks x no OpenMP threads
		10 285.84677 -3.4787531 0 -3.4418766 1611.7131
		20 248.14649 -3.4738884 0 -3.4418756 2312.0308
		30 198.94136 -3.4675394 0 -3.4418744 3168.1543
		40 152.74831 -3.4615791 0 -3.4418734 3903.5749
		50 121.9796 -3.4576091 0 -3.4418728 4387.1254
		60 113.27555 -3.4564863 0 -3.4418729 4556.3003
		70 125.68089 -3.4580873 0 -3.4418735 4431.2083
		80 151.47475 -3.4614159 0 -3.4418745 4107.2369
		90 179.18708 -3.4649919 0 -3.4418754 3739.5881
		100 197.50662 -3.4673559 0 -3.441876 3492.7778
		Loop time of 3.73974 on 4 procs for 100 steps with 512 atoms

		Performance: 1.155 ns/day, 20.776 hours/ns, 26.740 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 \| 4.8898 \| 4.907 \| 4.9329 \| 0.8 \| 98.27
		Pair \| 3.4687 \| 3.5182 \| 3.5985 \| 2.7 \| 94.07
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.058815 \| 0.084739 \| 0.1019 \| 6.1 \| 1.70
		Output \| 0.000252 \| 0.00038775 \| 0.000777 \| 0.0 \| 0.01
		Modify \| 0.000262 \| 0.00026675 \| 0.000272 \| 0.0 \| 0.01
		Other \| \| 0.001039 \| \| \| 0.02
		Comm \| 0.13897 \| 0.21952 \| 0.26888 \| 10.7 \| 5.87
		Output \| 0.00018191 \| 0.00047094 \| 0.0012944 \| 0.0 \| 0.01
		Modify \| 0.00013065 \| 0.00013524 \| 0.00014186 \| 0.0 \| 0.00
		Other \| \| 0.001456 \| \| \| 0.04

		Nlocal: 128 ave 128 max 128 min
		Histogram: 4 0 0 0 0 0 0 0 0 0
		@@ -153,4 +154,4 @@ Ave neighs/atom = 122
		Neighbor list builds = 0
		Dangerous builds = 0

		Total wall time: 0:00:05
		Total wall time: 0:00:03

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