Fix the example according to the convention (081839b4) · Commits · 郑智淋 / lammps

Original line number	Diff line number	Diff line
		# sample script to compare and debug GPU accelerated tip4p water
		# use '-sf gpu' to enables the GPU accelerated pair style
		# without it the original lj/cut/tip4p/long from module KSPACE will be used

		units real
		boundary p p p

		atom_style full
		bond_style harmonic
		angle_style harmonic
		atom_modify map array

		pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
		pair_modify table 0

		#long-range solver for TIP4P from module KSPACE works on CPU
		suffix off
		newton on
		kspace_style pppm/tip4p 1.0e-5
		suffix on

		read_data data.spce

		pair_coeff * * 0.0 0.0
		pair_coeff 1 1 0.1852 3.1589

		bond_coeff 1 0.0 0.9572
		angle_coeff 1 0.0 104.52

		group water type 1 2

		#maintain the water molecule rigid
		fix 1 water shake 1.0e-4 200 0 b 1 a 1
		fix 2 water nve

		thermo 100
		thermo_style custom step etotal ke pe temp evdwl ecoul elong press
		thermo_modify format float "%.15g"

		velocity water create 300 123

		if $(is_active(package,gpu)) &
		then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz"&
		else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
		dump_modify 11 sort id

		timestep 1

		run 1

examples/TIP4P/gpu_dump/log.19Dec19.tip4p.g++.1

0 → 100644

+127 −0

Original line number	Diff line number	Diff line
		LAMMPS (30 Oct 2019)
		#

		units real
		boundary p p p

		atom_style full
		bond_style harmonic
		angle_style harmonic
		atom_modify map array

		pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0
		pair_modify table 0

		#long-range solver for TIP4P from module KSPACE works on CPU
		suffix off
		newton on
		kspace_style pppm/tip4p 1.0e-5
		suffix on

		read_data data.spce
		orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		4500 atoms
		scanning bonds ...
		2 = max bonds/atom
		scanning angles ...
		1 = max angles/atom
		reading bonds ...
		3000 bonds
		reading angles ...
		1500 angles
		2 = max # of 1-2 neighbors
		1 = max # of 1-3 neighbors
		1 = max # of 1-4 neighbors
		2 = max # of special neighbors
		special bonds CPU = 0.00143709 secs
		read_data CPU = 0.0185545 secs

		pair_coeff * * 0.0 0.0
		pair_coeff 1 1 0.1852 3.1589

		bond_coeff 1 0.0 0.9572
		angle_coeff 1 0.0 104.52

		group water type 1 2
		4500 atoms in group water

		#maintain the water molecule rigid
		fix 1 water shake 1.0e-4 200 0 b 1 a 1
		0 = # of size 2 clusters
		0 = # of size 3 clusters
		0 = # of size 4 clusters
		1500 = # of frozen angles
		fix 2 water nve

		thermo 100
		thermo_style custom step etotal ke pe temp evdwl ecoul elong press
		thermo_modify format float "%.15g"

		velocity water create 300 123

		if $(is_active(package,gpu)) then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
		if 0 then "dump 11 all custom 1 dump.force_gpu id type x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz"
		dump 11 all custom 1 dump.force_cpu id type x y z fx fy fz
		dump_modify 11 sort id

		timestep 1

		run 1
		PPPM initialization ...
		extracting TIP4P info from pair style
		using polynomial approximation for long-range coulomb (../kspace.cpp:323)
		G vector (1/distance) = 0.342797
		grid = 36 36 36
		stencil order = 5
		estimated absolute RMS force accuracy = 0.00261362
		estimated relative force accuracy = 7.87083e-06
		using double precision KISS FFT
		3d grid and FFT values/proc = 79507 46656
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 11.3092
		ghost atom cutoff = 11.3092
		binsize = 5.6546, bins = 7 7 7
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair lj/cut/tip4p/long, 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) = 30.18 \| 30.18 \| 30.18 Mbytes
		Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press
		0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273
		1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061
		Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms

		Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s
		101.7% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.071838 \| 0.071838 \| 0.071838 \| 0.0 \| 76.10
		Bond \| 1.974e-06 \| 1.974e-06 \| 1.974e-06 \| 0.0 \| 0.00
		Kspace \| 0.012686 \| 0.012686 \| 0.012686 \| 0.0 \| 13.44
		Neigh \| 0 \| 0 \| 0 \| 0.0 \| 0.00
		Comm \| 0.00012462 \| 0.00012462 \| 0.00012462 \| 0.0 \| 0.13
		Output \| 0.0093175 \| 0.0093175 \| 0.0093175 \| 0.0 \| 9.87
		Modify \| 0.00038138 \| 0.00038138 \| 0.00038138 \| 0.0 \| 0.40
		Other \| \| 4.484e-05 \| \| \| 0.05

		Nlocal: 4500 ave 4500 max 4500 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 15219 ave 15219 max 15219 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 1371514
		Ave neighs/atom = 304.781
		Ave special neighs/atom = 2
		Neighbor list builds = 0
		Dangerous builds = 0
		Total wall time: 0:00:00

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