Merge pull request #415 from stanmoore1/kk_qeq

Add neigh/qeq option to Kokkos package

doc/src/package.txt

@@ -62,12 +62,13 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
-      {neigh} value = {full} or {half} or {n2} or {full/cluster}
+      {neigh} value = {full} or {half}
+        full = full neighbor list
+        half = half neighbor list built in thread-safe manner
+      {neigh/qeq} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
-        n2 = non-binning neighbor list build, O(N^2) algorithm
-        full/cluster = full neighbor list with clustered groups of atoms
       {newton} = {off} or {on}
         off = set Newton pairwise and bonded flags off (default)
         on = set Newton pairwise and bonded flags on
@@ -392,10 +393,7 @@ default value as listed below.
 
 The {neigh} keyword determines how neighbor lists are built.  A value
 of {half} uses a thread-safe variant of half-neighbor lists,
-the same as used by most pair styles in LAMMPS.  A value of
+the same as used by most pair styles in LAMMPS.
-{n2} uses an O(N^2) algorithm to build the neighbor list without
-binning, where N = # of atoms on a processor.  It is typically slower
-than the other methods, which use binning.
 
 A value of {full} uses a full neighbor lists and is the default.  This
 performs twice as much computation as the {half} option, however that
@@ -403,15 +401,9 @@ is often a win because it is thread-safe and doesn't require atomic
 operations in the calculation of pair forces.  For that reason, {full}
 is the default setting.  However, when running in MPI-only mode with 1
 thread per MPI task, {half} neighbor lists will typically be faster,
-just as it is for non-accelerated pair styles.
+just as it is for non-accelerated pair styles. Similarly, the {neigh/qeq}
-
+keyword determines how neighbor lists are built for "fix qeq/reax/kk"_fix_qeq_reax.html.
-A value of {full/cluster} is an experimental neighbor style, where
+If not explicitly set, the value of {neigh/qeq} will match {neigh}.
-particles interact with all particles within a small cluster, if at
-least one of the clusters particles is within the neighbor cutoff
-range.  This potentially allows for better vectorization on
-architectures such as the Intel Phi.  If also reduces the size of the
-neighbor list by roughly a factor of the cluster size, thus reducing
-the total memory footprint considerably.
 
 The {newton} keyword sets the Newton flags for pairwise and bonded
 interactions to {off} or {on}, the same as the "newton"_newton.html
@@ -582,9 +574,9 @@ is used.  If it is not used, you must invoke the package intel
 command in your input script or or via the "-pk intel" "command-line
 switch"_Section_start.html#start_7.
 
-For the KOKKOS package, the option defaults neigh = full, newton =
+For the KOKKOS package, the option defaults neigh = full, neigh/qeq
-off, binsize = 0.0, and comm = device.  These settings are made
+ = full, newton = off, binsize = 0.0, and comm = device.  These settings
-automatically by the required "-k on" "command-line
+ are made automatically by the required "-k on" "command-line
 switch"_Section_start.html#start_7.  You can change them bu using the
 package kokkos command in your input script or via the "-pk kokkos"
 "command-line switch"_Section_start.html#start_7.

src/KOKKOS/fix_qeq_reax_kokkos.cpp

@@ -82,7 +82,7 @@ void FixQEqReaxKokkos<DeviceType>::init()
 
   FixQEqReax::init();
 
-  neighflag = lmp->kokkos->neighflag;
+  neighflag = lmp->kokkos->neighflag_qeq;
   int irequest = neighbor->nrequest - 1;
   
   neighbor->requests[irequest]->

src/KOKKOS/kokkos.cpp

@@ -119,6 +119,8 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   // default settings for package kokkos command
 
   neighflag = FULL;
+  neighflag_qeq = FULL;
+  neighflag_qeq_set = 0;
   exchange_comm_classic = 0;
   forward_comm_classic = 0;
   exchange_comm_on_host = 0;
@@ -152,6 +154,8 @@ void KokkosLMP::accelerator(int narg, char **arg)
   // defaults
 
   neighflag = FULL;
+  neighflag_qeq = FULL;
+  neighflag_qeq_set = 0;
   int newtonflag = 0;
   double binsize = 0.0;
   exchange_comm_classic = forward_comm_classic = 0;
@@ -169,6 +173,19 @@ void KokkosLMP::accelerator(int narg, char **arg)
           neighflag = HALF;
       } else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
       else error->all(FLERR,"Illegal package kokkos command");
+      if (!neighflag_qeq_set) neighflag_qeq = neighflag;
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"neigh/qeq") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command");
+      if (strcmp(arg[iarg+1],"full") == 0) neighflag_qeq = FULL;
+      else if (strcmp(arg[iarg+1],"half") == 0) {
+        if (num_threads > 1 || ngpu > 0)
+          neighflag_qeq = HALFTHREAD;
+        else 
+          neighflag_qeq = HALF;
+      } else if (strcmp(arg[iarg+1],"n2") == 0) neighflag_qeq = N2;
+      else error->all(FLERR,"Illegal package kokkos command");
+      neighflag_qeq_set = 1;
       iarg += 2;
     } else if (strcmp(arg[iarg],"binsize") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command");

src/KOKKOS/kokkos.h

@@ -23,6 +23,8 @@ class KokkosLMP : protected Pointers {
  public:
   int kokkos_exists;
   int neighflag;
+  int neighflag_qeq;
+  int neighflag_qeq_set;
   int exchange_comm_classic;
   int forward_comm_classic;
   int exchange_comm_on_host;