re-enable perpertual neighborlist for compute entropy/atom if avg flag is used only (275626a1) · Commits · 郑智淋 / lammps

examples/USER/misc/entropy/log.entropy

+37 −35

Original line number	Original line	Diff line number	Diff line
	LAMMPS (4 Jan 2019)		LAMMPS (18 Feb 2020)

	units metal		units metal
	atom_style full		atom_style full
	@@ -6,7 +6,7 @@ atom_style full
	read_data data.interface		read_data data.interface
	Reading data file ...		Reading data file ...
	triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0)		triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0)
	4 by 1 by 1 MPI processor grid		1 by 1 by 1 MPI processor grid
	reading atoms ...		reading atoms ...
	4096 atoms		4096 atoms
	reading velocities ...		reading velocities ...
	@@ -18,6 +18,8 @@ Finding 1-2 1-3 1-4 neighbors ...
	0 = max # of 1-3 neighbors		0 = max # of 1-3 neighbors
	0 = max # of 1-4 neighbors		0 = max # of 1-4 neighbors
	1 = max # of special neighbors		1 = max # of special neighbors
			special bonds CPU = 0.00048995 secs
			read_data CPU = 0.0104239 secs
	mass 1 22.98977		mass 1 22.98977

	neigh_modify delay 10 every 1		neigh_modify delay 10 every 1
	@@ -45,28 +47,28 @@ fix 1 all nph x 1. 1. 10.
	fix 2 all temp/csvr 350. 350. 0.1 64582		fix 2 all temp/csvr 350. 350. 0.1 64582

	run 1000		run 1000
	WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)		WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
	WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)		WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
	WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)		WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
	WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)		WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
	Neighbor list info ...		Neighbor list info ...
	update every 1 steps, delay 10 steps, check yes		update every 1 steps, delay 10 steps, check yes
	max neighbors/atom: 2000, page size: 100000		max neighbors/atom: 2000, page size: 100000
	master list distance cutoff = 13.2		master list distance cutoff = 13.2
	ghost atom cutoff = 13.2		ghost atom cutoff = 13.2
	binsize = 6.6, bins = 21 6 6		binsize = 6.6, bins = 21 6 6
	5 neighbor lists, perpetual/occasional/extra = 5 0 0		5 neighbor lists, perpetual/occasional/extra = 3 2 0
	(1) pair eam/fs, perpetual, half/full from (2)		(1) pair eam/fs, perpetual
	attributes: half, newton on		attributes: half, newton on
	pair build: halffull/newton		pair build: half/bin/newton/tri
			stencil: half/bin/3d/newton/tri
			bin: standard
			(2) compute entropy/atom, occasional, copy from (4)
			attributes: full, newton on
			pair build: copy
	stencil: none		stencil: none
	bin: none		bin: none
	(2) compute entropy/atom, perpetual		(3) compute entropy/atom, occasional, copy from (4)
	attributes: full, newton on
	pair build: full/bin
	stencil: full/bin/3d
	bin: standard
	(3) compute entropy/atom, perpetual, copy from (2)
	attributes: full, newton on		attributes: full, newton on
	pair build: copy		pair build: copy
	stencil: none		stencil: none
	@@ -85,35 +87,35 @@ Setting up Verlet run ...
	Unit style : metal		Unit style : metal
	Current step : 0		Current step : 0
	Time step : 0.002		Time step : 0.002
	Per MPI rank memory allocation (min/avg/max) = 19.6 \| 19.6 \| 19.6 Mbytes		Per MPI rank memory allocation (min/avg/max) = 58.81 \| 58.81 \| 58.81 Mbytes
	Step Temp E_pair E_mol TotEng Press Volume		Step Temp E_pair E_mol TotEng Press Volume
	0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75		0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75
	500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09		500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09
	1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86		1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86
	Loop time of 4.4394 on 4 procs for 1000 steps with 4096 atoms		Loop time of 20.309 on 1 procs for 1000 steps with 4096 atoms

	Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s		Performance: 8.509 ns/day, 2.821 hours/ns, 49.239 timesteps/s
	99.5% CPU use with 4 MPI tasks x no OpenMP threads		99.4% CPU use with 1 MPI tasks x no OpenMP threads

	MPI task timing breakdown:		MPI task timing breakdown:
	Section \| min time \| avg time \| max time \|%varavg\| %total		Section \| min time \| avg time \| max time \|%varavg\| %total
	---------------------------------------------------------------		---------------------------------------------------------------
	Pair \| 3.5298 \| 3.5931 \| 3.6669 \| 2.6 \| 80.94		Pair \| 17.851 \| 17.851 \| 17.851 \| 0.0 \| 87.89
	Bond \| 8.2099e-05 \| 0.00011444 \| 0.00014673 \| 0.0 \| 0.00		Bond \| 0.00029588 \| 0.00029588 \| 0.00029588 \| 0.0 \| 0.00
	Neigh \| 0.43384 \| 0.4445 \| 0.45558 \| 1.4 \| 10.01		Neigh \| 1.5377 \| 1.5377 \| 1.5377 \| 0.0 \| 7.57
	Comm \| 0.048904 \| 0.11122 \| 0.16728 \| 12.7 \| 2.51		Comm \| 0.083142 \| 0.083142 \| 0.083142 \| 0.0 \| 0.41
	Output \| 0.22595 \| 0.22595 \| 0.22596 \| 0.0 \| 5.09		Output \| 0.59598 \| 0.59598 \| 0.59598 \| 0.0 \| 2.93
	Modify \| 0.053103 \| 0.053795 \| 0.054549 \| 0.3 \| 1.21		Modify \| 0.20727 \| 0.20727 \| 0.20727 \| 0.0 \| 1.02
	Other \| \| 0.01068 \| \| \| 0.24		Other \| \| 0.03411 \| \| \| 0.17

	Nlocal: 1024 ave 1040 max 1001 min		Nlocal: 4096 ave 4096 max 4096 min
	Histogram: 1 0 0 0 0 0 2 0 0 1		Histogram: 1 0 0 0 0 0 0 0 0 0
	Nghost: 4614.25 ave 4700 max 4540 min		Nghost: 11116 ave 11116 max 11116 min
	Histogram: 1 1 0 0 0 0 0 1 0 1		Histogram: 1 0 0 0 0 0 0 0 0 0
	Neighs: 121747 ave 126398 max 116930 min		Neighs: 486987 ave 486987 max 486987 min
	Histogram: 1 0 0 1 0 0 1 0 0 1		Histogram: 1 0 0 0 0 0 0 0 0 0
	FullNghs: 243494 ave 252523 max 233841 min		FullNghs: 973974 ave 973974 max 973974 min
	Histogram: 1 0 0 1 0 0 1 0 0 1		Histogram: 1 0 0 0 0 0 0 0 0 0

	Total # of neighbors = 973974		Total # of neighbors = 973974
	Ave neighs/atom = 237.787		Ave neighs/atom = 237.787
	@@ -121,4 +123,4 @@ Ave special neighs/atom = 0
	Neighbor list builds = 13		Neighbor list builds = 13
	Dangerous builds = 0		Dangerous builds = 0

	Total wall time: 0:00:04		Total wall time: 0:00:20

src/USER-MISC/compute_entropy_atom.cpp

+6 −4

Original line number	Original line	Diff line number	Diff line
	@@ -141,12 +141,14 @@ void ComputeEntropyAtom::init()
	neighbor->requests[irequest]->compute = 1;		neighbor->requests[irequest]->compute = 1;
	neighbor->requests[irequest]->half = 0;		neighbor->requests[irequest]->half = 0;
	neighbor->requests[irequest]->full = 1;		neighbor->requests[irequest]->full = 1;
	neighbor->requests[irequest]->occasional = 1;
	if (avg_flag) {		if (avg_flag) {
	// need a full neighbor list with neighbors of the ghost atoms		// need a full neighbor list with neighbors of the ghost atoms
			neighbor->requests[irequest]->occasional = 0;
	neighbor->requests[irequest]->ghost = 1;		neighbor->requests[irequest]->ghost = 1;
	} else {		} else {
	// need a full neighbor list		// need a regular full neighbor list
			// can build it occasionally
			neighbor->requests[irequest]->occasional = 1;
	neighbor->requests[irequest]->ghost = 0;		neighbor->requests[irequest]->ghost = 0;
	}		}

	@@ -196,9 +198,9 @@ void ComputeEntropyAtom::compute_peratom()
	}		}
	}		}

	// invoke full neighbor list (will copy or build if necessary)		// invoke occasional neighbor list build (if not perpetual)

	neighbor->build_one(list);		if (!avg_flag) neighbor->build_one(list);

	inum = list->inum + list->gnum;		inum = list->inum + list->gnum;
	ilist = list->ilist;		ilist = list->ilist;

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