Merge pull request #1309 from PabloPiaggi/pair_entropy (0e1c6082) · Commits · 郑智淋 / lammps

examples/USER/misc/entropy/log.entropy

+34 −34

Original line number	Diff line number	Diff line
		LAMMPS (30 Mar 2018)
		LAMMPS (4 Jan 2019)

		units metal
		atom_style full
		@@ -45,10 +45,10 @@ fix 1 all nph x 1. 1. 10.
		fix 2 all temp/csvr 350. 350. 0.1 64582

		run 1000
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
		WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		@@ -56,27 +56,27 @@ Neighbor list info ...
		ghost atom cutoff = 13.2
		binsize = 6.6, bins = 21 6 6
		5 neighbor lists, perpetual/occasional/extra = 5 0 0
		(1) pair eam/fs, perpetual
		(1) pair eam/fs, perpetual, half/full from (2)
		attributes: half, newton on
		pair build: half/bin/newton/tri
		stencil: half/bin/3d/newton/tri
		bin: standard
		pair build: halffull/newton
		stencil: none
		bin: none
		(2) compute entropy/atom, perpetual
		attributes: full, newton on, ghost
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		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, ghost
		attributes: full, newton on
		pair build: copy
		stencil: none
		bin: none
		(4) compute entropy/atom, perpetual, copy from (2)
		(4) compute entropy/atom, perpetual
		attributes: full, newton on, ghost
		pair build: copy
		stencil: none
		bin: none
		(5) compute entropy/atom, perpetual, copy from (2)
		pair build: full/bin/ghost
		stencil: full/ghost/bin/3d
		bin: standard
		(5) compute entropy/atom, perpetual, copy from (4)
		attributes: full, newton on, ghost
		pair build: copy
		stencil: none
		@@ -85,34 +85,34 @@ Setting up Verlet run ...
		Unit style : metal
		Current step : 0
		Time step : 0.002
		Per MPI rank memory allocation (min/avg/max) = 25.68 \| 25.69 \| 25.69 Mbytes
		Per MPI rank memory allocation (min/avg/max) = 19.6 \| 19.6 \| 19.6 Mbytes
		Step Temp E_pair E_mol TotEng Press Volume
		0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75
		500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18
		1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18
		Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms
		500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09
		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

		Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s
		99.8% CPU use with 4 MPI tasks x no OpenMP threads
		Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s
		99.5% CPU use with 4 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 4.2832 \| 4.3257 \| 4.3839 \| 1.8 \| 80.95
		Bond \| 0.00018309 \| 0.00019825 \| 0.00021418 \| 0.0 \| 0.00
		Neigh \| 0.42195 \| 0.42512 \| 0.42739 \| 0.3 \| 7.96
		Comm \| 0.051679 \| 0.1101 \| 0.14916 \| 10.8 \| 2.06
		Output \| 0.40909 \| 0.4091 \| 0.40911 \| 0.0 \| 7.66
		Modify \| 0.060869 \| 0.061921 \| 0.06327 \| 0.4 \| 1.16
		Other \| \| 0.01161 \| \| \| 0.22
		Pair \| 3.5298 \| 3.5931 \| 3.6669 \| 2.6 \| 80.94
		Bond \| 8.2099e-05 \| 0.00011444 \| 0.00014673 \| 0.0 \| 0.00
		Neigh \| 0.43384 \| 0.4445 \| 0.45558 \| 1.4 \| 10.01
		Comm \| 0.048904 \| 0.11122 \| 0.16728 \| 12.7 \| 2.51
		Output \| 0.22595 \| 0.22595 \| 0.22596 \| 0.0 \| 5.09
		Modify \| 0.053103 \| 0.053795 \| 0.054549 \| 0.3 \| 1.21
		Other \| \| 0.01068 \| \| \| 0.24

		Nlocal: 1024 ave 1040 max 1001 min
		Histogram: 1 0 0 0 0 0 2 0 0 1
		Nghost: 4614.25 ave 4700 max 4540 min
		Histogram: 1 1 0 0 0 0 0 1 0 1
		Neighs: 121747 ave 126398 max 116931 min
		Neighs: 121747 ave 126398 max 116930 min
		Histogram: 1 0 0 1 0 0 1 0 0 1
		FullNghs: 243494 ave 252523 max 233842 min
		FullNghs: 243494 ave 252523 max 233841 min
		Histogram: 1 0 0 1 0 0 1 0 0 1

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

		Total wall time: 0:00:05
		Total wall time: 0:00:04

src/USER-MISC/compute_entropy_atom.cpp

+9 −3

Original line number	Diff line number	Diff line
		@@ -65,6 +65,7 @@ ComputeEntropyAtom(LAMMPS lmp, int narg, char *arg) :
		if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
		" command; cutoff must be positive");

		cutoff2 = 0.;
		avg_flag = 0;
		local_flag = 0;

		@@ -137,15 +138,20 @@ void ComputeEntropyAtom::init()
		if (count > 1 && comm->me == 0)
		error->warning(FLERR,"More than one compute entropy/atom");

		// need a full neighbor list with neighbors of the ghost atoms

		// Request neighbor list
		int irequest = neighbor->request(this,instance_me);
		neighbor->requests[irequest]->pair = 0;
		neighbor->requests[irequest]->compute = 1;
		neighbor->requests[irequest]->half = 0;
		neighbor->requests[irequest]->full = 1;
		neighbor->requests[irequest]->occasional = 0;
		if (avg_flag) {
		// need a full neighbor list with neighbors of the ghost atoms
		neighbor->requests[irequest]->ghost = 1;
		} else {
		// need a full neighbor list
		neighbor->requests[irequest]->ghost = 0;
		}

		}

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