change purge target in Makefile, also fixed one issue with Make.py

examples/tad/README

@@ -1,5 +1,5 @@
 Run this example as:
 
-mpirun -np 3 lmp_linux -partition 3x1 -in in.tad
+mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad
 
 You should be able to use any number of replicas >= 3.

src/KOKKOS/comm_tiled_kokkos.cpp

@@ -0,0 +1,266 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <string.h>
+#include "comm_tiled_kokkos.h"
+#include "comm_brick.h"
+#include "atom_kokkos.h"
+#include "atom_vec.h"
+#include "domain.h"
+#include "force.h"
+#include "pair.h"
+#include "neighbor.h"
+#include "modify.h"
+#include "fix.h"
+#include "compute.h"
+#include "output.h"
+#include "dump.h"
+#include "memory.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+
+#define BUFFACTOR 1.5
+#define BUFFACTOR 1.5
+#define BUFMIN 1000
+#define BUFEXTRA 1000
+#define EPSILON 1.0e-6
+
+#define DELTA_PROCS 16
+
+enum{SINGLE,MULTI};               // same as in Comm
+enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};    // several files
+
+/* ---------------------------------------------------------------------- */
+
+CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+//IMPORTANT: we *MUST* pass "*oldcomm" to the Comm initializer here, as
+//           the code below *requires* that the (implicit) copy constructor
+//           for Comm is run and thus creating a shallow copy of "oldcomm".
+//           The call to Comm::copy_arrays() then converts the shallow copy
+//           into a deep copy of the class with the new layout.
+
+CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp, Comm *oldcomm) : CommTiled(lmp,oldcomm)
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+CommTiledKokkos::~CommTiledKokkos()
+{
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+
+/* ----------------------------------------------------------------------
+   forward communication of atom coords every timestep
+   other per-atom attributes may also be sent via pack/unpack routines
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm(int dummy)
+{
+  if (comm_x_only) {
+    atomKK->sync(Host,X_MASK);
+    atomKK->modified(Host,X_MASK);
+  } else if (ghost_velocity) {
+    atomKK->sync(Host,X_MASK | V_MASK);
+    atomKK->modified(Host,X_MASK | V_MASK);
+  } else {
+    atomKK->sync(Host,ALL_MASK);
+    atomKK->modified(Host,ALL_MASK);
+  }
+
+  CommTiled::forward_comm(dummy);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication of forces on atoms every timestep
+   other per-atom attributes may also be sent via pack/unpack routines
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm()
+{
+  if (comm_f_only)
+    atomKK->sync(Host,F_MASK);
+  else
+    atomKK->sync(Host,ALL_MASK);
+  CommTiled::reverse_comm();
+  if (comm_f_only)
+    atomKK->modified(Host,F_MASK);
+  else
+    atomKK->modified(Host,ALL_MASK);
+  atomKK->sync(Device,ALL_MASK);
+}
+
+/* ----------------------------------------------------------------------
+   exchange: move atoms to correct processors
+   atoms exchanged with procs that touch sub-box in each of 3 dims
+   send out atoms that have left my box, receive ones entering my box
+   atoms will be lost if not inside a touching proc's box
+     can happen if atom moves outside of non-periodic bounary
+     or if atom moves more than one proc away
+   this routine called before every reneighboring
+   for triclinic, atoms must be in lamda coords (0-1) before exchange is called
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::exchange()
+{
+  atomKK->sync(Host,ALL_MASK);
+  CommTiled::exchange();
+  atomKK->modified(Host,ALL_MASK);
+}
+
+/* ----------------------------------------------------------------------
+   borders: list nearby atoms to send to neighboring procs at every timestep
+   one list is created per swap/proc that will be made
+   as list is made, actually do communication
+   this does equivalent of a forward_comm(), so don't need to explicitly
+     call forward_comm() on reneighboring timestep
+   this routine is called before every reneighboring
+   for triclinic, atoms must be in lamda coords (0-1) before borders is called
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::borders()
+{
+  atomKK->sync(Host,ALL_MASK);
+  CommTiled::borders();
+  atomKK->modified(Host,ALL_MASK);
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Pair
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm_pair(Pair *pair)
+{
+  CommTiled::forward_comm_pair(pair);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Pair
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm_pair(Pair *pair)
+{
+  CommTiled::reverse_comm_pair(pair);
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Fix
+   size/nsize used only to set recv buffer limit
+   size = 0 (default) -> use comm_forward from Fix
+   size > 0 -> Fix passes max size per atom
+   the latter is only useful if Fix does several comm modes,
+     some are smaller than max stored in its comm_forward
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm_fix(Fix *fix, int size)
+{
+  CommTiled::forward_comm_fix(fix,size);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Fix
+   size/nsize used only to set recv buffer limit
+   size = 0 (default) -> use comm_forward from Fix
+   size > 0 -> Fix passes max size per atom
+   the latter is only useful if Fix does several comm modes,
+     some are smaller than max stored in its comm_forward
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm_fix(Fix *fix, int size)
+{
+  CommTiled::reverse_comm_fix(fix,size);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Fix with variable size data
+   query fix for all pack sizes to insure buf_send is big enough
+   handshake sizes before irregular comm to insure buf_recv is big enough
+   NOTE: how to setup one big buf recv with correct offsets ??
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm_fix_variable(Fix *fix)
+{
+  CommTiled::reverse_comm_fix_variable(fix);
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Compute
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm_compute(Compute *compute)
+{
+  CommTiled::forward_comm_compute(compute);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Compute
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm_compute(Compute *compute)
+{
+  CommTiled::reverse_comm_compute(compute);
+}
+
+/* ----------------------------------------------------------------------
+   forward communication invoked by a Dump
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm_dump(Dump *dump)
+{
+  CommTiled::forward_comm_dump(dump);
+}
+
+/* ----------------------------------------------------------------------
+   reverse communication invoked by a Dump
+   nsize used only to set recv buffer limit
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::reverse_comm_dump(Dump *dump)
+{
+  CommTiled::reverse_comm_dump(dump);
+}
+
+/* ----------------------------------------------------------------------
+   forward communication of Nsize values in per-atom array
+------------------------------------------------------------------------- */
+
+void CommTiledKokkos::forward_comm_array(int nsize, double **array)
+{
+  CommTiled::forward_comm_array(nsize,array);
+}
+
+/* ----------------------------------------------------------------------
+   exchange info provided with all 6 stencil neighbors
+   NOTE: this method is currently not used
+------------------------------------------------------------------------- */
+
+int CommTiledKokkos::exchange_variable(int n, double *inbuf, double *&outbuf)
+{
+  CommTiled::exchange_variable(n,inbuf,outbuf);
+}

src/KOKKOS/comm_tiled_kokkos.h

@@ -0,0 +1,59 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_COMM_TILED_KOKKOS_H
+#define LMP_COMM_TILED_KOKKOS_H
+
+#include "comm_tiled.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+class CommTiledKokkos : public CommTiled {
+ public:
+  CommTiledKokkos(class LAMMPS *);
+  CommTiledKokkos(class LAMMPS *, class Comm *);
+  virtual ~CommTiledKokkos();
+
+  void forward_comm(int dummy = 0);    // forward comm of atom coords
+  void reverse_comm();                 // reverse comm of forces
+  void exchange();                     // move atoms to new procs
+  void borders();                      // setup list of atoms to comm
+
+  void forward_comm_pair(class Pair *);    // forward comm from a Pair
+  void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
+  void forward_comm_fix(class Fix *, int size=0);
+                                                   // forward comm from a Fix
+  void reverse_comm_fix(class Fix *, int size=0);
+                                                   // reverse comm from a Fix
+  void reverse_comm_fix_variable(class Fix *);
+                                     // variable size reverse comm from a Fix
+  void forward_comm_compute(class Compute *);  // forward from a Compute
+  void reverse_comm_compute(class Compute *);  // reverse from a Compute
+  void forward_comm_dump(class Dump *);    // forward comm from a Dump
+  void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
+
+  void forward_comm_array(int, double **);          // forward comm of array
+  int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
+
+ private:
+
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+*/

src/KOKKOS/neighbor_kokkos.cpp

@@ -280,15 +280,19 @@ void NeighborKokkos::choose_build(int index, NeighRequest *rq)
   if (rq->kokkos_host != 0) {
     PairPtrHost pb = NULL;
     if (rq->ghost) {
-      if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
+      if (rq->full) {
-      else if (rq->half) &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
+        if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
-      pair_build_host[index] = pb;
+        else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
+      }
+      else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
     } else {
-      if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
+      if (rq->full) {
+        if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
+        else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
+      }
       else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,0>;
-      pair_build_host[index] = pb;
     }
-    return;
+    pair_build_host[index] = pb;
   }
   if (rq->kokkos_device != 0) {
     PairPtrDevice pb = NULL;

src/Make.py

@@ -26,7 +26,8 @@ libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
 buildclasses = ("intel","kokkos")
 makeclasses = ("cc","flags","mpi","fft","jpg","png")
 
-setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall","exceptions","#exceptions")
+setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig",
+           "smallsmall","exceptions","#exceptions")
 actionargs = ("lib-all","file","clean","exe")
 
 gpubuildflag = 0
@@ -85,7 +86,8 @@ def switch2str(switches,switch_order):
 def compile_check(compiler,ccflags,warn):
   open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
   tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)
-  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
+  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
+                                     shell=True).decode()
   except subprocess.CalledProcessError as e: txt = e.output
   flag = 1
   if txt or not os.path.isfile("tmpauto.o"):
@@ -105,7 +107,8 @@ def compile_check(compiler,ccflags,warn):
 def link_check(linker,linkflags,libs,warn):
   open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")
   tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)
-  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()
+  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,
+                                     shell=True).decode()
   except subprocess.CalledProcessError as e: txt = e.output
   flag = 1
   if txt or not os.path.isfile("tmpauto"):
@@ -532,7 +535,8 @@ class Actions(object):
     
     if caller == "file" or "file" not in self.alist:
       # make certain that 'MAKE/MINE' folder exists.
-      subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,stderr=subprocess.STDOUT,shell=True)
+      subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,
+                              stderr=subprocess.STDOUT,shell=True)
       make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
       print("Created src/MAKE/MINE/Makefile.auto")
       
@@ -859,9 +863,12 @@ class Packages(object):
     if self.plist: print("Installing packages ...")
     for one in self.plist:
       if one == "orig": continue
-      subprocess.check_output("cd %s; make %s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
+      subprocess.check_output("cd %s; make %s" % (dir.src,one),
+                              stderr=subprocess.STDOUT,shell=True)
     if self.plist and verbose:
-      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
+      txt = subprocess.check_output("cd %s; make ps" % dir.src,
+                                    stderr=subprocess.STDOUT,
+                                    shell=True).decode()
       print("Package status after installation:")
       print(txt)
       
@@ -871,12 +878,16 @@ class Packages(object):
   def uninstall(self):
     if not self.plist or self.plist[-1] != "orig": return
     print("Restoring packages to original state ...")
-    subprocess.check_output("cd %s; make no-all" % dir.src,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make no-all" % dir.src,
+                            stderr=subprocess.STDOUT,shell=True)
     for one in self.all:
       if self.original[one]:
-        subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)
+        subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),
+                                stderr=subprocess.STDOUT,shell=True)
     if verbose:
-      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()
+      txt = subprocess.check_output("cd %s; make ps" % dir.src,
+                                    stderr=subprocess.STDOUT,
+                                    shell=True).decode()
       print("Restored package status:")
       print(txt)
       
@@ -970,7 +981,8 @@ class Settings(object):
   def help(self):
     return """
 -s set1 set2 ...
-  possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall exceptions #exceptions
+  possible settings = gzip #gzip ffmpeg #ffmpeg
+                      smallbig bigbig smallsmall exceptions #exceptions
   alter LAMMPS ifdef settings in Makefile.auto
     only happens if new Makefile.auto is created by use of "file" action
   gzip and #gzip turn on/off LAMMPS_GZIP setting
@@ -1059,7 +1071,8 @@ class ATC(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
     
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" %
+                            libdir,stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
     
@@ -1110,7 +1123,8 @@ class AWPMD(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" %
+                            libdir,stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
 
@@ -1161,7 +1175,8 @@ class COLVARS(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" %
+                            libdir,stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
 
@@ -1213,7 +1228,8 @@ class CUDA(object):
           
   def build(self): 
     libdir = dir.lib + "/cuda"
-    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make clean" % libdir,
+                            stderr=subprocess.STDOUT,shell=True)
     if self.mode == "double": n = 2
     elif self.mode == "mixed": n = 3
     elif self.mode == "single": n = 1
@@ -1308,7 +1324,8 @@ class GPU(object):
     make = "make"
     if "shannon" == platform.node(): make = "srun make"
 
-    subprocess.check_output("cd %s; %s -f Makefile.auto clean" % (libdir,make),stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; %s -f Makefile.auto clean" %
+                            (libdir,make),stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
     else: txt = "cd %s; %s -f Makefile.auto" % (libdir,make)
 
@@ -1359,7 +1376,8 @@ class H5MD(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make clean" % libdir,
+                            stderr=subprocess.STDOUT,shell=True)
     txt = "cd %s; make" % libdir
 
     # if verbose, print output as build proceeds, else only print if fails
@@ -1409,7 +1427,8 @@ class MEAM(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" %
+                            libdir,stderr=subprocess.STDOUT,shell=True)
     # do not use -j for MEAM build, parallel build does not work
     txt = "cd %s; make -f Makefile.auto" % libdir
 
@@ -1460,7 +1479,8 @@ class POEMS(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,
+                            stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
 
@@ -1506,9 +1526,10 @@ class PYTHON(object):
     libdir = dir.lib + "/python"
     if self.lammpsflag:
       subprocess.check_output("cd %s; cp Makefile.lammps.%s Makefile.lammps" %
-                         (libdir,self.lammps))
+                              (libdir,self.lammps))
     if not os.path.isfile("%s/Makefile.lammps.%s" % (libdir,self.lammps)):
-      error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" % self.lammps)
+      error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" %
+            self.lammps)
     else: print("Created lib/python/Makefile.lammps file")
 
 # QMMM lib
@@ -1546,7 +1567,8 @@ class QMMM(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)
+    subprocess.check_output("cd %s; make -f Makefile.auto clean" %
+                            libdir,stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
 
@@ -1597,7 +1619,8 @@ class REAX(object):
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    cmd = "cd %s; make -f Makefile.auto clean" % libdir
+    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
     if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
     else: txt = "cd %s; make -f Makefile.auto" % libdir
     
@@ -1643,7 +1666,8 @@ class VORONOI(object):
     if not self.install: return
     libdir = dir.lib + "/voronoi"
     cmd = "cd %s; python install.py %s" % (libdir,self.install)
-    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True).decode()
+    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,
+                                  shell=True).decode()
     if verbose: print(txt)
     print("Created lib/voronoi library")
 

src/Makefile

@@ -92,7 +92,7 @@ help:
 	@echo 'make package-update (pu) replace src files with updated package files'
 	@echo 'make package-overwrite   replace package files with src files'
 	@echo 'make package-diff (pd)   diff src files against package files'
-	@echo 'make package-purge       purge obsolete copies of package sources'
+	@echo 'make purge               purge obsolete copies of source files'
 	@echo ''
 	@echo 'make machine             build LAMMPS for machine'
 	@echo 'make mode=lib machine    build LAMMPS as static lib for machine'
@@ -314,7 +314,7 @@ package-diff pd:
 	@echo ''
 	@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done
 
-package-purge: Purge.list
+purge: Purge.list
 	@echo 'Purging obsolete and auto-generated source files'
 	@for f in `grep -v '#' Purge.list` ;		\
 	    do test -f $$f && rm $$f && echo $$f || : ;		\

src/USER-REAXC/pair_reax_c.cpp

@@ -348,7 +348,7 @@ void PairReaxC::init_style( )
 
   int iqeq;
   for (iqeq = 0; iqeq < modify->nfix; iqeq++)
-    if (strcmp(modify->fix[iqeq]->style,"qeq/reax") == 0) break;
+    if (strstr(modify->fix[iqeq]->style,"qeq/reax")) break;
   if (iqeq == modify->nfix && qeqflag == 1)
     error->all(FLERR,"Pair reax/c requires use of fix qeq/reax");
 

src/comm_tiled.cpp

@@ -45,9 +45,6 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};    // several files
 
 CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
 {
-  if (lmp->kokkos)
-    error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");
-
   style = 1;
   layout = LAYOUT_UNIFORM;
   pbc_flag = NULL;
@@ -63,9 +60,6 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
 
 CommTiled::CommTiled(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
 {
-  if (lmp->kokkos)
-    error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");
-
   style = 1;
   layout = oldcomm->layout;
   Comm::copy_arrays(oldcomm);

src/comm_tiled.h

@@ -26,26 +26,26 @@ class CommTiled : public Comm {
 
   void init();
   void setup();                        // setup comm pattern
-  void forward_comm(int dummy = 0);    // forward comm of atom coords
+  virtual void forward_comm(int dummy = 0);    // forward comm of atom coords
-  void reverse_comm();                 // reverse comm of forces
+  virtual void reverse_comm();                 // reverse comm of forces
-  void exchange();                     // move atoms to new procs
+  virtual void exchange();                     // move atoms to new procs
-  void borders();                      // setup list of atoms to comm
+  virtual void borders();                      // setup list of atoms to comm
 
-  void forward_comm_pair(class Pair *);    // forward comm from a Pair
+  virtual void forward_comm_pair(class Pair *);    // forward comm from a Pair
-  void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
+  virtual void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
   virtual void forward_comm_fix(class Fix *, int size=0);
                                                    // forward comm from a Fix
   virtual void reverse_comm_fix(class Fix *, int size=0);
                                                    // reverse comm from a Fix
   virtual void reverse_comm_fix_variable(class Fix *);
                                      // variable size reverse comm from a Fix
-  void forward_comm_compute(class Compute *);  // forward from a Compute
+  virtual void forward_comm_compute(class Compute *);  // forward from a Compute
-  void reverse_comm_compute(class Compute *);  // reverse from a Compute
+  virtual void reverse_comm_compute(class Compute *);  // reverse from a Compute
-  void forward_comm_dump(class Dump *);    // forward comm from a Dump
+  virtual void forward_comm_dump(class Dump *);    // forward comm from a Dump
-  void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
+  virtual void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
 
-  void forward_comm_array(int, double **);          // forward comm of array
+  virtual void forward_comm_array(int, double **);          // forward comm of array
-  int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
+  virtual int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
 
   void coord2proc_setup();
   int coord2proc(double *, int &, int &, int &);