git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12630 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-REAXC/reaxc_ffield.cpp

@@ -45,7 +45,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
   comm = MPI_COMM_WORLD;
 
   /* open force field file */
-  if ( (fp = fopen( ffield_file, "r" ) ) == NULL ) {
+  if ( (fp = lmp_open_potential( ffield_file ) ) == NULL ) {
     fprintf( stderr, "error opening the force field file! terminating...\n" );
     MPI_Abort( comm, FILE_NOT_FOUND );
   }

src/USER-REAXC/reaxc_tool_box.cpp

@@ -238,3 +238,76 @@ void sfree( void *ptr, const char *name )
   free( ptr );
   ptr = NULL;
 }
+
+/* ----------------------------------------------------------------------
+   strip off leading part of path, return just the filename
+------------------------------------------------------------------------- */
+
+static const char *potname(const char *path)
+{
+  const char *pot;
+
+  if (path == NULL) return NULL;
+
+#if defined(_WIN32)
+  // skip over the disk drive part of windows pathnames
+  if (isalpha(path[0]) && path[1] == ':') 
+    path += 2;
+#endif
+
+  for (pot = path; *path != '\0'; ++path) {
+#if defined(_WIN32)
+    if ((*path == '\\') || (*path == '/')) pot = path + 1;
+#else
+    if (*path == '/') pot = path + 1;
+#endif
+  }
+
+  return pot;
+}
+
+/* ----------------------------------------------------------------------
+   open a potential file as specified by name; failing that,
+   search in dir specified by env variable LAMMPS_POTENTIALS
+------------------------------------------------------------------------- */
+
+FILE *lmp_open_potential(const char *name)
+{
+  FILE *fp;
+
+  if (name == NULL) return NULL;
+
+  // attempt to open file directly
+  // if successful, return ptr
+
+  fp = fopen(name,"r");
+  if (fp) return fp;
+
+  // try the environment variable directory
+
+  const char *path = getenv("LAMMPS_POTENTIALS");
+  if (path == NULL) return NULL;
+
+  const char *pot = potname(name);
+  if (pot == NULL) return NULL;
+
+  size_t len1 = strlen(path);
+  size_t len2 = strlen(pot);
+  char *newpath = new char[len1+len2+2];
+
+  strcpy(newpath,path);
+#if defined(_WIN32)
+  newpath[len1] = '\\';
+  newpath[len1+1] = 0;
+#else
+  newpath[len1] = '/';
+  newpath[len1+1] = 0;
+#endif
+  strcat(newpath,pot);
+
+  fp = fopen(newpath,"r");
+  delete[] newpath;
+  return fp;
+}
+
+

src/USER-REAXC/reaxc_tool_box.h

@@ -64,5 +64,5 @@ int   Tokenize( char*, char*** );
 void *smalloc( long, const char*, MPI_Comm );
 void *scalloc( int, int, const char*, MPI_Comm );
 void sfree( void*, const char* );
-
+FILE *lmp_open_potential(const char *);
 #endif

src/fix_nh.cpp

@@ -836,12 +836,13 @@ void FixNH::final_integrate()
   nve_v();
 
   // re-compute temp before nh_v_press()
-  // only needed for temperature computes with BIAS:
+  // only needed for temperature computes with BIAS on reneighboring steps:
   //   b/c some biases store per-atom values (e.g. temp/profile) 
   //   per-atom values are invalid if reneigh/comm occurred
   //     since temp->compute() in initial_integrate()
 
-  if (which == BIAS) t_current = temperature->compute_scalar();
+  if (which == BIAS && neighbor->ago == 0) 
+    t_current = temperature->compute_scalar();
 
   if (pstat_flag) nh_v_press();