git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14270 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Manual.txt

@@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
 
 .. toctree::
    :maxdepth: 2
-   :numbered:
+   :numbered: // comment
    
    Section_intro
    Section_start
@@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`search`
+* :ref:`genindex` // comment
+* :ref:`search` // comment
    
 END_RST -->
 

python/lammps.py

@@ -121,22 +121,23 @@ class lammps:
   # double was allocated by library interface function
   
   def extract_fix(self,id,style,type,i=0,j=0):
-    if type == 0:
-      if style > 0: return None
+    if style == 0:
       self.lib.lammps_extract_fix.restype = POINTER(c_double)
       ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
       result = ptr[0]
       self.lib.lammps_free(ptr)
       return result
-    if type == 1:
-      self.lib.lammps_extract_fix.restype = POINTER(c_double)
+    elif (style == 1) or (style == 2):
+      if type == 1:
+        self.lib.lammps_extract_fix.restype = POINTER(c_double)
+      elif type == 2:
+        self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
+      else:
+        return None
       ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
       return ptr
-    if type == 2:
-      self.lib.lammps_extract_fix.restype = POINTER(POINTER(c_double))
-      ptr = self.lib.lammps_extract_fix(self.lmp,id,style,type,i,j)
-      return ptr
-    return None
+    else:
+      return None
 
   # free memory for 1 double or 1 vector of doubles via lammps_free()
   # for vector, must copy nlocal returned values to local c_double vector

src/USER-MISC/pair_srp.cpp

@@ -73,10 +73,22 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
 
   nextra = 1;
   segment = NULL;
+
+  // generate unique fix-id for this pair style instance
   fix_id = strdup("XX_FIX_SRP");
   fix_id[0] = '0' + srp_instance / 10;
   fix_id[1] = '0' + srp_instance % 10;
   ++srp_instance;
+
+  // create fix SRP instance here, as it has to
+  // be executed before all other fixes
+  char **fixarg = new char*[3];
+  fixarg[0] = fix_id;
+  fixarg[1] = (char *) "all";
+  fixarg[2] = (char *) "SRP";
+  modify->add_fix(3,fixarg);
+  f_srp = (FixSRP *) modify->fix[modify->nfix-1];
+  delete [] fixarg;
 }
 
 /* ----------------------------------------------------------------------
@@ -436,16 +448,10 @@ void PairSRP::init_style()
   if (!force->newton_pair)
     error->all(FLERR,"PairSRP: Pair srp requires newton pair on");
 
-  // need fix srp
-  // invoke here instead of constructor
-  // to make restart possible
-  char **fixarg = new char*[3];
-  fixarg[0] = fix_id;
-  fixarg[1] = (char *) "all";
-  fixarg[2] = (char *) "SRP";
-  modify->add_fix(3,fixarg);
-  f_srp = (FixSRP *) modify->fix[modify->nfix-1];
-  delete [] fixarg;
+  // verify that fix SRP is still defined and has not been changed.
+  int ifix = modify->find_fix(fix_id);
+  if (f_srp != (FixSRP *)modify->fix[ifix])
+    error->all(FLERR,"Fix SRP has been changed unexpectedly");
 
   // set bond type in fix srp
   // bonds of this type will be represented by bond particles

src/library.cpp

@@ -435,8 +435,7 @@ void lammps_gather_atoms(void *ptr, char *name,
     if (count == 1) vector = (int *) vptr;
     else array = (int **) vptr;
 
-    int *copy;
-    lmp->memory->create(copy,count*natoms,"lib/gather:copy");
+    int *copy = (int*) data;
     for (i = 0; i < count*natoms; i++) copy[i] = 0;
 
     tagint *tag = lmp->atom->tag;
@@ -452,8 +451,7 @@ void lammps_gather_atoms(void *ptr, char *name,
           copy[offset++] = array[i][0];
       }
 
-    MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
-    lmp->memory->destroy(copy);
+    MPI_Allreduce(MPI_IN_PLACE,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
 
   } else {
     double *vector = NULL;
@@ -461,8 +459,7 @@ void lammps_gather_atoms(void *ptr, char *name,
     if (count == 1) vector = (double *) vptr;
     else array = (double **) vptr;
 
-    double *copy;
-    lmp->memory->create(copy,count*natoms,"lib/gather:copy");
+    double *copy = (double*) data;
     for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
 
     tagint *tag = lmp->atom->tag;
@@ -479,8 +476,7 @@ void lammps_gather_atoms(void *ptr, char *name,
       }
     }
 
-    MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
-    lmp->memory->destroy(copy);
+    MPI_Allreduce(MPI_IN_PLACE,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
   }
 }