make pair style momb example follow LAMMPS conventions more closely (865b41e2) · Commits · 郑智淋 / lammps

examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs

100755 → 100644

+0 −0

File mode changed from 100755 to 100644.

examples/USER/misc/momb/system.in→examples/USER/misc/momb/in.system

+7 −9

Original line number	Diff line number	Diff line
		@@ -11,7 +11,7 @@ angle_style charmm
		dihedral_style charmm
		improper_style harmonic
		pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
		kspace_style pppm 1e-4
		kspace_style pppm 1e-5

		# ----------------- Atom Definition Section -----------------

		@@ -166,15 +166,13 @@ special_bonds charmm

		timestep 0.001

		restart 2000 NVT.restart.1_dup NVT.restart.1

		minimize 1.0e-3 1.0e-5 1000 10000
		reset_timestep 0

		velocity all create 413.0 12378 dist gaussian

		thermo 0
		thermo_style custom step pe ke etotal temp vol press lx lz pxx pyy pzz
		thermo_modify flush yes
		thermo 10
		thermo_style custom step pe ke etotal temp press pxx pyy pzz

		variable STEP equal step
		variable PE equal pe
		@@ -190,8 +188,8 @@ variable PYY equal pyy
		variable PZZ equal pzz

		fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
		fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
		#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"

		dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
		#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz

		run 100

examples/USER/misc/momb/log.momb→examples/USER/misc/momb/log.17Mar2017.system.g++.1

+97 −65

Original line number	Diff line number	Diff line
		LAMMPS (17 Nov 2016)
		LAMMPS (17 Mar 2017)
		using 1 OpenMP thread(s) per MPI task

		# ----------------- Settings Section -----------------
		@@ -13,7 +13,7 @@ angle_style charmm
		dihedral_style charmm
		improper_style harmonic
		pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
		kspace_style pppm 1e-4
		kspace_style pppm 1e-5

		# ----------------- Atom Definition Section -----------------

		@@ -192,73 +192,96 @@ special_bonds charmm

		timestep 0.001

		restart 2000 NVT.restart.1_dup NVT.restart.1

		minimize 1.0e-3 1.0e-5 1000 10000
		PPPM initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
		G vector (1/distance) = 0.187769
		grid = 16 16 40
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		G vector (1/distance) = 0.224856
		grid = 27 27 64
		stencil order = 5
		estimated absolute RMS force accuracy = 0.00139106
		estimated relative force accuracy = 9.66035e-05
		using single precision FFTs
		3d grid and FFT values/proc = 19845 10240
		estimated absolute RMS force accuracy = 0.00015081
		estimated relative force accuracy = 1.04732e-05
		using double precision FFTs
		3d grid and FFT values/proc = 79764 46656
		WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
		Neighbor list info ...
		5 neighbor list requests
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 14
		ghost atom cutoff = 14
		binsize = 7 -> bins = 8 8 23
		Memory usage per processor = 48.6138 Mbytes
		binsize = 7, bins = 8 8 23
		5 neighbor lists, perpetual/occasional/extra = 5 0 0
		(1) pair eam/fs, perpetual, skip from (5)
		attributes: half, newton on
		pair build: skip
		stencil: none
		bin: none
		(2) pair lj/charmm/coul/long, perpetual, skip from (5)
		attributes: half, newton on
		pair build: skip
		stencil: none
		bin: none
		(3) pair momb, perpetual, skip from (5)
		attributes: half, newton on
		pair build: skip
		stencil: none
		bin: none
		(4) pair morse, perpetual, copy from (3)
		attributes: half, newton on
		pair build: copy
		stencil: none
		bin: none
		(5) neighbor class addition, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 99.82 \| 99.82 \| 99.82 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 0 -10041.86 218.18376 -9823.6761 -1155.6237
		9 0 -10251.809 211.33378 -10040.475 -3384.1678
		Loop time of 2.01938 on 1 procs for 9 steps with 18146 atoms
		0 0 -10035.476 218.18376 -9817.2917 -1066.914
		9 0 -10244.892 211.35072 -10033.541 -3283.8636
		Loop time of 2.65996 on 1 procs for 9 steps with 18146 atoms

		99.7% CPU use with 1 MPI tasks x no OpenMP threads
		99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

		Minimization stats:
		Stopping criterion = energy tolerance
		Energy initial, next-to-last, final =
		-9823.67611001 -10030.895598 -10040.4750172
		Force two-norm initial, final = 76.9199 27.3415
		Force max component initial, final = 11.8655 7.37992
		Final line search alpha, max atom move = 0.0472487 0.348692
		-9817.29174185 -10023.887559 -10033.5413886
		Force two-norm initial, final = 76.9233 27.3547
		Force max component initial, final = 11.8658 7.37882
		Final line search alpha, max atom move = 0.0472944 0.348977
		Iterations, force evaluations = 9 11

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 1.6622 \| 1.6622 \| 1.6622 \| 0.0 \| 82.31
		Bond \| 0.054745 \| 0.054745 \| 0.054745 \| 0.0 \| 2.71
		Kspace \| 0.11761 \| 0.11761 \| 0.11761 \| 0.0 \| 5.82
		Neigh \| 0.16836 \| 0.16836 \| 0.16836 \| 0.0 \| 8.34
		Comm \| 0.0029683 \| 0.0029683 \| 0.0029683 \| 0.0 \| 0.15
		Pair \| 2.2936 \| 2.2936 \| 2.2936 \| 0.0 \| 86.23
		Bond \| 0.08754 \| 0.08754 \| 0.08754 \| 0.0 \| 3.29
		Kspace \| 0.2664 \| 0.2664 \| 0.2664 \| 0.0 \| 10.02
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.0041108 \| 0.0041108 \| 0.0041108 \| 0.0 \| 0.15
		Output \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Modify \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Other \| \| 0.01347 \| \| \| 0.67
		Other \| \| 0.008299 \| \| \| 0.31

		Nlocal: 18146 ave 18146 max 18146 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 29277 ave 29277 max 29277 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 5.49017e+06 ave 5.49017e+06 max 5.49017e+06 min
		Neighs: 439189 ave 439189 max 439189 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 5490167
		Ave neighs/atom = 302.555
		Total # of neighbors = 439189
		Ave neighs/atom = 24.2031
		Ave special neighs/atom = 5.92362
		Neighbor list builds = 1
		Neighbor list builds = 0
		Dangerous builds = 0
		reset_timestep 0

		velocity all create 413.0 12378 dist gaussian

		thermo 0
		thermo_style custom step pe ke etotal temp vol press lx lz pxx pyy pzz
		thermo_modify flush yes
		thermo 10
		thermo_style custom step pe ke etotal temp press pxx pyy pzz

		variable STEP equal step
		variable PE equal pe
		@@ -274,52 +297,61 @@ variable PYY equal pyy
		variable PZZ equal pzz

		fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
		fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
		#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"

		dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
		#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz

		run 100
		PPPM initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
		G vector (1/distance) = 0.187769
		grid = 16 16 40
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
		G vector (1/distance) = 0.224856
		grid = 27 27 64
		stencil order = 5
		estimated absolute RMS force accuracy = 0.00139106
		estimated relative force accuracy = 9.66035e-05
		using single precision FFTs
		3d grid and FFT values/proc = 19845 10240
		estimated absolute RMS force accuracy = 0.00015081
		estimated relative force accuracy = 1.04732e-05
		using double precision FFTs
		3d grid and FFT values/proc = 79764 46656
		WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
		Memory usage per processor = 45.2388 Mbytes
		Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz
		9 -10040.475 968.66066 -9071.8144 413 460013.27 -1135.0076 53.6198 160 5128.2409 -4940.1319 -3593.1317
		109 -9552.3639 560.57156 -8991.7924 239.00636 460013.27 -1193.1308 53.6198 160 1847.8619 -3035.3718 -2391.8825
		Loop time of 13.4379 on 1 procs for 100 steps with 18146 atoms
		Per MPI rank memory allocation (min/avg/max) = 96.44 \| 96.44 \| 96.44 Mbytes
		Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
		0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
		10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
		20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
		30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
		40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
		50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
		60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
		70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
		80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
		90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
		100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
		Loop time of 18.4128 on 1 procs for 100 steps with 18146 atoms

		Performance: 0.643 ns/day, 37.327 hours/ns, 7.442 timesteps/s
		99.8% CPU use with 1 MPI tasks x no OpenMP threads
		Performance: 0.469 ns/day, 51.147 hours/ns, 5.431 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 \| 10.731 \| 10.731 \| 10.731 \| 0.0 \| 79.85
		Bond \| 0.40862 \| 0.40862 \| 0.40862 \| 0.0 \| 3.04
		Kspace \| 0.98401 \| 0.98401 \| 0.98401 \| 0.0 \| 7.32
		Neigh \| 0.87771 \| 0.87771 \| 0.87771 \| 0.0 \| 6.53
		Comm \| 0.022856 \| 0.022856 \| 0.022856 \| 0.0 \| 0.17
		Output \| 0.36853 \| 0.36853 \| 0.36853 \| 0.0 \| 2.74
		Modify \| 0.032646 \| 0.032646 \| 0.032646 \| 0.0 \| 0.24
		Other \| \| 0.01276 \| \| \| 0.09
		Pair \| 14.225 \| 14.225 \| 14.225 \| 0.0 \| 77.26
		Bond \| 0.65464 \| 0.65464 \| 0.65464 \| 0.0 \| 3.56
		Kspace \| 2.22 \| 2.22 \| 2.22 \| 0.0 \| 12.06
		Neigh \| 1.1926 \| 1.1926 \| 1.1926 \| 0.0 \| 6.48
		Comm \| 0.040519 \| 0.040519 \| 0.040519 \| 0.0 \| 0.22
		Output \| 0.0023048 \| 0.0023048 \| 0.0023048 \| 0.0 \| 0.01
		Modify \| 0.058326 \| 0.058326 \| 0.058326 \| 0.0 \| 0.32
		Other \| \| 0.01913 \| \| \| 0.10

		Nlocal: 18146 ave 18146 max 18146 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 29123 ave 29123 max 29123 min
		Nghost: 29127 ave 29127 max 29127 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 5.50412e+06 ave 5.50412e+06 max 5.50412e+06 min
		Neighs: 441898 ave 441898 max 441898 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 5504118
		Ave neighs/atom = 303.324
		Total # of neighbors = 441898
		Ave neighs/atom = 24.3524
		Ave special neighs/atom = 5.92362
		Neighbor list builds = 5
		Dangerous builds = 0
		Total wall time: 0:00:16
		Total wall time: 0:00:22

examples/USER/misc/momb/log.17Mar2017.system.g++.4

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