sync with SVN (31204aab) · Commits · 郑智淋 / lammps

doc/src/Manual.txt

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		<!-- HTML_ONLY -->
		<HEAD>
		<TITLE>LAMMPS Users Manual</TITLE>
		<META NAME="docnumber" CONTENT="27 Oct 2016 version">
		<META NAME="docnumber" CONTENT="4 Nov 2016 version">
		<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
		<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
		</HEAD>
		@@ -21,7 +21,7 @@
		<H1></H1>

		LAMMPS Documentation :c,h3
		27 Oct 2016 version :c,h4
		4 Nov 2016 version :c,h4

		Version info: :h4

+4 −5

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		@@ -15,7 +15,7 @@ pair_style snap :pre
		[Examples:]

		pair_style snap
		pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
		pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre

		[Description:]

		@@ -27,7 +27,7 @@ it uses bispectrum components
		to characterize the local neighborhood of each atom
		in a very general way. The mathematical definition of the
		bispectrum calculation used by SNAP is identical
		to that used of "compute sna/atom"_compute_sna_atom.html.
		to that used by "compute sna/atom"_compute_sna_atom.html.
		In SNAP, the total energy is decomposed into a sum over
		atom energies. The energy of atom {i } is
		expressed as a weighted sum over bispectrum components.
		@@ -183,8 +183,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
		:line

		:link(Thompson2014)
		[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
		available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
		[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).

		:link(Bartok2010)
		[(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

+3 −3

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		@@ -6,12 +6,12 @@ SHELL = /bin/sh
		# compiler/linker settings
		# specify flags and libraries needed for your compiler

		CC = mpiicpc
		CC = mpicxx
		CCFLAGS = -g -O3
		SHFLAGS = -fPIC
		DEPFLAGS = -M

		LINK = mpiicpc
		LINK = mpicxx
		LINKFLAGS = -g -O3
		LIB =
		SIZE = size
		@@ -20,7 +20,7 @@ ARCHIVE = ar
		ARFLAGS = -rc
		SHLIBFLAGS = -shared
		KOKKOS_DEVICES = OpenMP
		KOKKOS_ARCH = KNC
		KOKKOS_ARCH = KNL

		# ---------------------------------------------------------------------
		# LAMMPS-specific settings, all OPTIONAL

+9 −0

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		@@ -22,6 +22,7 @@
		#include "kokkos.h"
		#include "atom_kokkos.h"
		#include "comm_kokkos.h"
		#include "comm_tiled_kokkos.h"
		#include "domain_kokkos.h"
		#include "neighbor_kokkos.h"
		#include "modify_kokkos.h"
		@@ -33,6 +34,7 @@

		#include "atom.h"
		#include "comm_brick.h"
		#include "comm_tiled.h"
		#include "domain.h"
		#include "neighbor.h"
		#include "modify.h"
		@@ -68,6 +70,13 @@ class CommKokkos : public CommBrick {
		~CommKokkos() {}
		};

		class CommTiledKokkos : public CommTiled {
		public:
		CommTiledKokkos(class LAMMPS *lmp) : CommTiled(lmp) {}
		CommTiledKokkos(class LAMMPS lmp, Comm oldcomm) : CommTiled(lmp,oldcomm) {}
		~CommTiledKokkos() {}
		};

		class DomainKokkos : public Domain {
		public:
		DomainKokkos(class LAMMPS *lmp) : Domain(lmp) {}

+5 −1

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		@@ -27,6 +27,7 @@
		#include "comm.h"
		#include "comm_brick.h"
		#include "comm_tiled.h"
		#include "accelerator_kokkos.h"
		#include "group.h"
		#include "domain.h"
		#include "output.h"
		@@ -1465,7 +1466,10 @@ void Input::comm_style()
		} else if (strcmp(arg[0],"tiled") == 0) {
		if (comm->style == 1) return;
		Comm *oldcomm = comm;
		comm = new CommTiled(lmp,oldcomm);

		if (lmp->kokkos) comm = new CommTiledKokkos(lmp,oldcomm);
		else comm = new CommTiled(lmp,oldcomm);

		delete oldcomm;
		} else error->all(FLERR,"Illegal comm_style command");
		}