From 5f86c15dd224a1affb857634e397ccca94d01e26 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 27 Apr 2016 14:56:23 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14895
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/Make.py                    | 15 ++++++++++-----
 src/USER-OMP/fix_omp.cpp       |  4 ++--
 src/USER-REAXC/pair_reax_c.cpp |  4 ++--
 src/compute_temp_partial.cpp   |  8 +++++++-
 src/fix_nh.cpp                 |  4 ++--
 5 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/src/Make.py b/src/Make.py
index 8e57c7491b..e42c703b8c 100755
--- a/src/Make.py
+++ b/src/Make.py
@@ -287,11 +287,10 @@ class Actions:
           else: wrapper = cc.wrap
           abbrev = cc.abbrev
           if abbrev == "mpi":
-            txt = commands.getoutput("mpicxx -show")
-            if "-lmpich" in txt:
+            if cc.parent == "mpich":
               make.addvar("CC","-cxx=%s" % wrapper)
               make.addvar("LINK","-cxx=%s" % wrapper)
-            elif "-lmpi" in txt:
+            elif cc.parent == "openmpi":
               make.addvar("export OMPI_CXX",wrapper,"cc")
               precompiler = "env OMPI_CXX=%s " % wrapper
             else: error("Could not add MPI wrapper compiler, " +
@@ -1716,10 +1715,11 @@ class Cc:
     self.inlist = copy.copy(list)
     self.compiler = self.abbrev = ""
     self.wrap = ""
+    self.parent = ""
 
   def help(self):
     return """
--cc compiler wrap=wcompiler
+-cc compiler wrap=wcompiler,parent
   alter CC setting in Makefile.auto
     only happens if new Makefile.auto is created by use of "file" action
   compiler is required, all other args are optional
@@ -1729,6 +1729,8 @@ class Cc:
     mpi by itself is changed to mpicxx
   wcompiler = compiler for mpi wrapper to use
     use nvcc for building for Kokkos/cuda with provided nvcc_wrapper
+  parent = openmpi or mpich
+    parent style determines syntax for setting low-level compiler
 """
 
   def check(self):
@@ -1750,9 +1752,12 @@ class Cc:
     for one in self.inlist[1:]:
       words = one.split('=')
       if len(words) != 2: error("-cc args are invalid")
+      args = words[1].split(',')
+      if len(args) != 2: error("-cc args are invalid")
       if words[0] == "wrap":
         if self.abbrev != "mpi": error("-cc compiler is not a wrapper")
-        self.wrap = words[1]
+        self.wrap = args[0]
+        self.parent = args[1]
       else: error("-cc args are invalid")
 
 # Flags class
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 7cb63bcc16..cd90ef6e15 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -102,8 +102,8 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
   while (iarg < narg) {
     if (strcmp(arg[iarg],"neigh") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal package omp command");
-      if (strcmp(arg[iarg]+1,"yes") == 0) _neighbor = true;
-      else if (strcmp(arg[iarg]+1,"no") == 0) _neighbor = false;
+      if (strcmp(arg[iarg+1],"yes") == 0) _neighbor = true;
+      else if (strcmp(arg[iarg+1],"no") == 0) _neighbor = false;
       else error->all(FLERR,"Illegal package omp command");
       iarg += 2;
     } else error->all(FLERR,"Illegal package omp command");
diff --git a/src/USER-REAXC/pair_reax_c.cpp b/src/USER-REAXC/pair_reax_c.cpp
index dc977249fc..352a9468b3 100644
--- a/src/USER-REAXC/pair_reax_c.cpp
+++ b/src/USER-REAXC/pair_reax_c.cpp
@@ -284,10 +284,10 @@ void PairReaxC::coeff( int nargs, char **args )
   fp = force->open_potential(file);
   if (fp != NULL)
     Read_Force_Field(fp, &(system->reax_param), control);
-  else if (comm->me == 0) {
+  else {
       char str[128];
       sprintf(str,"Cannot open ReaxFF potential file %s",file);
-      error->one(FLERR,str);
+      error->all(FLERR,str);
   }
 
   // read args that map atom types to elements in potential file
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index c4e8e7cd88..b330495c54 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -41,6 +41,9 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
   xflag = force->inumeric(FLERR,arg[3]);
   yflag = force->inumeric(FLERR,arg[4]);
   zflag = force->inumeric(FLERR,arg[5]);
+  if ((xflag != 0 && xflag != 1) || (yflag != 0 && yflag != 1)
+      || (zflag != 0 && zflag != 1))
+    error->all(FLERR,"Illegal compute temp/partial command");
   if (zflag && domain->dimension == 2)
     error->all(FLERR,"Compute temp/partial cannot use vz for 2d systemx");
 
@@ -77,7 +80,10 @@ void ComputeTempPartial::dof_compute()
   natoms_temp = group->count(igroup);
   int nper = xflag+yflag+zflag;
   dof = nper * natoms_temp;
-  dof -= (1.0*nper/domain->dimension)*fix_dof + extra_dof;
+
+  // distribute extra dofs evenly across active dimensions
+
+  dof -= (1.0*nper/domain->dimension)*(fix_dof + extra_dof);
   if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
   else tfactor = 0.0;
 }
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index 89bd562e8e..b300fd2d46 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -718,11 +718,11 @@ void FixNH::setup(int vflag)
   t_current = temperature->compute_scalar();
   tdof = temperature->dof;
   
-  // t_target is needed by NPH and NPT in compute_scalar()
+  // t_target is needed by NVT and NPT in compute_scalar()
   // If no thermostat or using fix nphug,
   // t_target must be defined by other means.
 
-  if (tstat_flag && strcmp(style,"nphug") != 0) {
+  if (tstat_flag && strstr(style,"nphug") == NULL) {
     compute_temp_target();
   } else if (pstat_flag) {