git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9206 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/atom.cpp

@@ -420,8 +420,8 @@ void Atom::modify_params(int narg, char **arg)
       iarg += 2;
     } else if (strcmp(arg[iarg],"sort") == 0) {
       if (iarg+3 > narg) error->all(FLERR,"Illegal atom_modify command");
-      sortfreq = atoi(arg[iarg+1]);
+      sortfreq = force->inumeric(arg[iarg+1]);
-      userbinsize = atof(arg[iarg+2]);
+      userbinsize = force->numeric(arg[iarg+2]);
       if (sortfreq < 0 || userbinsize < 0.0)
         error->all(FLERR,"Illegal atom_modify command");
       if (sortfreq >= 0 && firstgroupname)

src/fix.h

@@ -89,6 +89,7 @@ class Fix : protected Pointers {
   virtual void init_list(int, class NeighList *) {}
   virtual void setup(int) {}
   virtual void setup_pre_exchange() {}
+  virtual void setup_pre_neighbor() {}
   virtual void setup_pre_force(int) {}
   virtual void min_setup(int) {}
   virtual void initial_integrate(int) {}

src/min.cpp

@@ -235,6 +235,7 @@ void Min::setup()
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   domain->box_too_small_check();
+  modify->setup_pre_neighbor();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -321,6 +322,7 @@ void Min::setup_minimal(int flag)
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
     domain->box_too_small_check();
+    modify->setup_pre_neighbor();
     neighbor->build();
     neighbor->ncalls = 0;
   }

src/modify.cpp

@@ -245,6 +245,18 @@ void Modify::setup_pre_exchange()
       fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
 }
 
+/* ----------------------------------------------------------------------
+   setup pre_neighbor call, only for fixes that define pre_neighbor
+   called from Verlet, RESPA
+------------------------------------------------------------------------- */
+
+void Modify::setup_pre_neighbor()
+{
+  if (update->whichflag == 1)
+    for (int i = 0; i < n_pre_neighbor; i++)
+      fix[list_pre_neighbor[i]]->setup_pre_neighbor();
+}
+
 /* ----------------------------------------------------------------------
    setup pre_force call, only for fixes that define pre_force
    called from Verlet, RESPA, Min

src/modify.h

@@ -44,6 +44,7 @@ class Modify : protected Pointers {
   virtual void init();
   virtual void setup(int);
   virtual void setup_pre_exchange();
+  virtual void setup_pre_neighbor();
   virtual void setup_pre_force(int);
   virtual void initial_integrate(int);
   virtual void post_integrate();

src/respa.cpp

@@ -352,6 +352,7 @@ void Respa::setup()
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   domain->box_too_small_check();
+  modify->setup_pre_neighbor();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -417,6 +418,7 @@ void Respa::setup_minimal(int flag)
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
     domain->box_too_small_check();
+    modify->setup_pre_neighbor();
     neighbor->build();
     neighbor->ncalls = 0;
   }

src/verlet.cpp

@@ -112,6 +112,7 @@ void Verlet::setup()
   comm->borders();
   if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
   domain->box_too_small_check();
+  modify->setup_pre_neighbor();
   neighbor->build();
   neighbor->ncalls = 0;
 
@@ -169,6 +170,7 @@ void Verlet::setup_minimal(int flag)
     comm->borders();
     if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
     domain->box_too_small_check();
+    modify->setup_pre_neighbor();
     neighbor->build();
     neighbor->ncalls = 0;
   }