Update pair_kim to work with new neig. list Hints (7eeb96f1) · Commits · 郑智淋 / lammps

examples/kim/in.kim.lj

+2 −2

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@ variable zz equal 20*$z

		units metal
		atom_style atomic
		newton off

		lattice fcc 4.4300
		region box block 0 ${xx} 0 ${yy} 0 ${zz}
		@@ -24,9 +25,8 @@ create_atoms 1 box

		#pair_style lj/cut 8.1500
		#pair_coeff 1 1 0.0104 3.4000
		#pair_modify shift no

		pair_style kim LAMMPSvirial LennardJones_Ar
		pair_style kim KIMvirial LennardJones_Ar
		pair_coeff * * Ar

		mass 1 39.95

examples/kim/in.kim.lj.lmp

+1 −1

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ variable zz equal 20*$z

		units metal
		atom_style atomic
		newton off

		lattice fcc 4.4300
		region box block 0 ${xx} 0 ${yy} 0 ${zz}
		@@ -18,7 +19,6 @@ create_atoms 1 box

		pair_style lj/cut 8.1500
		pair_coeff 1 1 0.0104 3.4000
		pair_modify shift no

		#pair_style kim KIMvirial LennardJones_Ar
		#pair_coeff * * Ar

examples/kim/in.kim.lj.lmp.newton-on

0 → 100644

+35 −0

Original line number	Diff line number	Diff line
		# 3d Lennard-Jones melt

		variable x index 1
		variable y index 1
		variable z index 1

		variable xx equal 20*$x
		variable yy equal 20*$y
		variable zz equal 20*$z

		units metal
		atom_style atomic
		newton on

		lattice fcc 4.4300
		region box block 0 ${xx} 0 ${yy} 0 ${zz}
		create_box 1 box
		create_atoms 1 box

		pair_style lj/cut 8.1500
		pair_coeff 1 1 0.0104 3.4000

		#pair_style kim KIMvirial LennardJones_Ar
		#pair_coeff * * Ar

		mass 1 39.95
		velocity all create 200.0 232345 loop geom

		neighbor 0.3 bin
		neigh_modify delay 0 every 1 check yes

		fix 1 all nve
		#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0

		run 100

examples/kim/log.29Jun18.kim.lj.lmp.ubuntu.1→examples/kim/log.04Jul2018.kim.lj.lmp.newton-on.ubuntu.1

+21 −21

Original line number	Diff line number	Diff line
		--------------------------------------------------------------------------
		[[30970,1],0]: A high-performance Open MPI point-to-point messaging module
		[[19053,1],0]: A high-performance Open MPI point-to-point messaging module
		was unable to find any relevant network interfaces:

		Module: OpenFabrics (openib)
		@@ -16,13 +16,13 @@ Lattice spacing in x,y,z = 4.43 4.43 4.43
		Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
		1 by 1 by 1 MPI processor grid
		Created 32000 atoms
		Time spent = 0.0031676 secs
		Time spent = 0.00270113 secs
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 7.85482
		ghost atom cutoff = 7.85482
		binsize = 3.92741, bins = 23 23 23
		master list distance cutoff = 8.45
		ghost atom cutoff = 8.45
		binsize = 4.225, bins = 21 21 21
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut, perpetual
		attributes: half, newton on
		@@ -33,34 +33,34 @@ Setting up Verlet run ...
		Unit style : metal
		Current step : 0
		Time step : 0.001
		Per MPI rank memory allocation (min/avg/max) = 16.58 \| 16.58 \| 16.58 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 19.23 \| 19.23 \| 19.23 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 200 -495.29247 0 331.94661 -978.84224
		100 212.66365 -547.67175 0 331.94665 -1054.2086
		Loop time of 1.40245 on 1 procs for 100 steps with 32000 atoms
		0 200 6290.8194 0 7118.0584 129712.25
		100 95.179725 6718.814 0 7112.496 133346.59
		Loop time of 2.18554 on 1 procs for 100 steps with 32000 atoms

		Performance: 6.161 ns/day, 3.896 hours/ns, 71.304 timesteps/s
		100.0% CPU use with 1 MPI tasks x no OpenMP threads
		Performance: 3.953 ns/day, 6.071 hours/ns, 45.755 timesteps/s
		99.6% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.2556 \| 1.2556 \| 1.2556 \| 0.0 \| 89.53
		Neigh \| 0.098976 \| 0.098976 \| 0.098976 \| 0.0 \| 7.06
		Comm \| 0.011525 \| 0.011525 \| 0.011525 \| 0.0 \| 0.82
		Output \| 0.00021903 \| 0.00021903 \| 0.00021903 \| 0.0 \| 0.02
		Modify \| 0.023739 \| 0.023739 \| 0.023739 \| 0.0 \| 1.69
		Other \| \| 0.01244 \| \| \| 0.89
		Pair \| 2.0006 \| 2.0006 \| 2.0006 \| 0.0 \| 91.54
		Neigh \| 0.13933 \| 0.13933 \| 0.13933 \| 0.0 \| 6.38
		Comm \| 0.011122 \| 0.011122 \| 0.011122 \| 0.0 \| 0.51
		Output \| 0.00020978 \| 0.00020978 \| 0.00020978 \| 0.0 \| 0.01
		Modify \| 0.022358 \| 0.022358 \| 0.022358 \| 0.0 \| 1.02
		Other \| \| 0.01188 \| \| \| 0.54

		Nlocal: 32000 ave 32000 max 32000 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 19911 ave 19911 max 19911 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 1.36493e+06 ave 1.36493e+06 max 1.36493e+06 min
		Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 1364931
		Ave neighs/atom = 42.6541
		Total # of neighbors = 2126875
		Ave neighs/atom = 66.4648
		Neighbor list builds = 3
		Dangerous builds = 0
		Total wall time: 0:00:01
		Total wall time: 0:00:02

examples/kim/log.29Jun18.kim.lj.lmp.ubuntu.4→examples/kim/log.04Jul2018.kim.lj.lmp.newton-on.ubuntu.4

+26 −26

Original line number	Diff line number	Diff line
		--------------------------------------------------------------------------
		[[30962,1],0]: A high-performance Open MPI point-to-point messaging module
		[[19045,1],0]: A high-performance Open MPI point-to-point messaging module
		was unable to find any relevant network interfaces:

		Module: OpenFabrics (openib)
		@@ -16,13 +16,13 @@ Lattice spacing in x,y,z = 4.43 4.43 4.43
		Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
		1 by 2 by 2 MPI processor grid
		Created 32000 atoms
		Time spent = 0.00143054 secs
		Time spent = 0.00117056 secs
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 7.85482
		ghost atom cutoff = 7.85482
		binsize = 3.92741, bins = 23 23 23
		master list distance cutoff = 8.45
		ghost atom cutoff = 8.45
		binsize = 4.225, bins = 21 21 21
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut, perpetual
		attributes: half, newton on
		@@ -33,34 +33,34 @@ Setting up Verlet run ...
		Unit style : metal
		Current step : 0
		Time step : 0.001
		Per MPI rank memory allocation (min/avg/max) = 6.875 \| 6.875 \| 6.875 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 7.632 \| 7.632 \| 7.632 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 200 -495.29247 0 331.94661 -978.84224
		100 212.66365 -547.67175 0 331.94665 -1054.2086
		Loop time of 1.55473 on 4 procs for 100 steps with 32000 atoms
		0 200 6290.8194 0 7118.0584 129712.25
		100 95.179725 6718.814 0 7112.496 133346.59
		Loop time of 2.34104 on 4 procs for 100 steps with 32000 atoms

		Performance: 5.557 ns/day, 4.319 hours/ns, 64.320 timesteps/s
		23.8% CPU use with 4 MPI tasks x no OpenMP threads
		Performance: 3.691 ns/day, 6.503 hours/ns, 42.716 timesteps/s
		24.0% CPU use with 4 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.47168 \| 0.51922 \| 0.58923 \| 6.2 \| 33.40
		Neigh \| 0.061309 \| 0.077009 \| 0.10276 \| 5.7 \| 4.95
		Comm \| 0.87185 \| 0.92596 \| 0.95327 \| 3.4 \| 59.56
		Output \| 0.00035269 \| 0.00047555 \| 0.00055331 \| 0.0 \| 0.03
		Modify \| 0.0060711 \| 0.00616 \| 0.0062612 \| 0.1 \| 0.40
		Other \| \| 0.0259 \| \| \| 1.67
		Pair \| 0.91499 \| 0.96396 \| 1.0567 \| 5.6 \| 41.18
		Neigh \| 0.092245 \| 0.11781 \| 0.14572 \| 6.0 \| 5.03
		Comm \| 1.1264 \| 1.2287 \| 1.2906 \| 5.6 \| 52.49
		Output \| 0.00045199 \| 0.00051154 \| 0.00060273 \| 0.0 \| 0.02
		Modify \| 0.0058738 \| 0.0059629 \| 0.0061675 \| 0.2 \| 0.25
		Other \| \| 0.02406 \| \| \| 1.03

		Nlocal: 8000 ave 8014 max 7988 min
		Histogram: 1 0 0 1 1 0 0 0 0 1
		Nghost: 9131 ave 9143 max 9117 min
		Histogram: 1 0 0 0 0 1 1 0 0 1
		Neighs: 341233 ave 341715 max 340679 min
		Histogram: 1 0 0 0 1 0 0 1 0 1
		Nlocal: 8000 ave 8018 max 7967 min
		Histogram: 1 0 0 0 0 0 1 0 0 2
		Nghost: 9131 ave 9164 max 9113 min
		Histogram: 2 0 0 1 0 0 0 0 0 1
		Neighs: 531719 ave 533273 max 529395 min
		Histogram: 1 0 0 0 1 0 0 0 0 2

		Total # of neighbors = 1364931
		Ave neighs/atom = 42.6541
		Total # of neighbors = 2126875
		Ave neighs/atom = 66.4648
		Neighbor list builds = 3
		Dangerous builds = 0
		Total wall time: 0:00:01
		Total wall time: 0:00:02

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