ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

sync with SVN

Browse Source
This commit is contained in:
Steve Plimpton
2016-11-08 08:57:51 -07:00
parent 77bbf03f0f
commit 31204aab6a
6 changed files with 24 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/src/Manual.txt
View File

@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <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="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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
27 Oct 2016 version :c,h4 4 Nov 2016 version :c,h4
Version info: :h4 Version info: :h4

9
doc/src/pair_snap.txt
View File

@ -15,7 +15,7 @@ pair_style snap :pre
[Examples:] [Examples:]
pair_style snap 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:] [Description:]
@ -27,9 +27,9 @@ it uses bispectrum components
to characterize the local neighborhood of each atom to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the in a very general way. The mathematical definition of the
bispectrum calculation used by SNAP is identical 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 In SNAP, the total energy is decomposed into a sum over
atom energies. The energy of atom {i} is atom energies. The energy of atom {i } is
expressed as a weighted sum over bispectrum components. expressed as a weighted sum over bispectrum components.
:c,image(Eqs/pair_snap.jpg) :c,image(Eqs/pair_snap.jpg)
@ -183,8 +183,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:line :line
:link(Thompson2014) :link(Thompson2014)
[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint [(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).
available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
:link(Bartok2010) :link(Bartok2010)
[(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). [(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

6
src/MAKE/OPTIONS/Makefile.kokkos_phi
View File

@ -6,12 +6,12 @@ SHELL = /bin/sh
# compiler/linker settings # compiler/linker settings
# specify flags and libraries needed for your compiler # specify flags and libraries needed for your compiler
CC = mpiicpc CC = mpicxx
CCFLAGS = -g -O3 CCFLAGS = -g -O3
SHFLAGS = -fPIC SHFLAGS = -fPIC
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiicpc LINK = mpicxx
LINKFLAGS = -g -O3 LINKFLAGS = -g -O3
LIB = LIB =
SIZE = size SIZE = size
@ -20,7 +20,7 @@ ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SHLIBFLAGS = -shared SHLIBFLAGS = -shared
KOKKOS_DEVICES = OpenMP KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = KNC KOKKOS_ARCH = KNL
# --------------------------------------------------------------------- # ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL # LAMMPS-specific settings, all OPTIONAL

9
src/accelerator_kokkos.h
View File

@ -22,6 +22,7 @@
#include "kokkos.h" #include "kokkos.h"
#include "atom_kokkos.h" #include "atom_kokkos.h"
#include "comm_kokkos.h" #include "comm_kokkos.h"
#include "comm_tiled_kokkos.h"
#include "domain_kokkos.h" #include "domain_kokkos.h"
#include "neighbor_kokkos.h" #include "neighbor_kokkos.h"
#include "modify_kokkos.h" #include "modify_kokkos.h"
@ -33,6 +34,7 @@
#include "atom.h" #include "atom.h"
#include "comm_brick.h" #include "comm_brick.h"
#include "comm_tiled.h"
#include "domain.h" #include "domain.h"
#include "neighbor.h" #include "neighbor.h"
#include "modify.h" #include "modify.h"
@ -68,6 +70,13 @@ class CommKokkos : public CommBrick {
~CommKokkos() {} ~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 { class DomainKokkos : public Domain {
public: public:
DomainKokkos(class LAMMPS *lmp) : Domain(lmp) {} DomainKokkos(class LAMMPS *lmp) : Domain(lmp) {}

6
src/input.cpp
View File

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

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "27 Oct 2016" #define LAMMPS_VERSION "4 Nov 2016"