sync with SVN for creation of stable release

sync with SVN
2016-11-08 09:05:50 -07:00 · 2016-11-08 08:57:51 -07:00
6 changed files with 24 additions and 12 deletions
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="27 Oct 2016 version">
+<META NAME="docnumber" CONTENT="5 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
+5 Nov 2016 version :c,h4

 Version info: :h4

--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@ -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:]

@ -27,9 +27,9 @@ 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
+atom energies. The energy of atom {i } is
 expressed as a weighted sum over bispectrum components.

 :c,image(Eqs/pair_snap.jpg)
@ -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).
--- a/src/MAKE/OPTIONS/Makefile.kokkos_phi
+++ b/src/MAKE/OPTIONS/Makefile.kokkos_phi
@ -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
--- a/src/accelerator_kokkos.h
+++ b/src/accelerator_kokkos.h
@ -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) {}
--- a/src/input.cpp
+++ b/src/input.cpp
@ -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");
 }
--- a/src/version.h
+++ b/src/version.h
@ -1 +1 @@
-#define LAMMPS_VERSION "27 Oct 2016"
+#define LAMMPS_VERSION "5 Nov 2016"
Author	SHA1	Message	Date
Steve Plimpton	a23b287a7a	sync with SVN for creation of stable release	2016-11-08 09:05:50 -07:00
Steve Plimpton	31204aab6a	sync with SVN	2016-11-08 08:57:51 -07:00