changes in package files to match new find_custom() syntax

doc/src/fix_rigid.rst

@@ -64,7 +64,7 @@ Syntax
        *single* args = none
        *molecule* args = none
        *custom* args = *i_propname* or *v_varname*
-         i_propname = an integer property defined via fix property/atom
+         i_propname = a custom integer vector defined via fix property/atom
          v_varname  = an atom-style or atomfile-style variable
        *group* args = N groupID1 groupID2 ...
          N = # of groups
@@ -287,15 +287,16 @@ includes atoms you want to be part of rigid bodies.
 
 Bodystyle *custom* is similar to bodystyle *molecule* except that it
 is more flexible in using other per-atom properties to define the sets
-of atoms that form rigid bodies.  An integer vector defined by the
+of atoms that form rigid bodies.  A custom per-atom integer vector
-:doc:`fix property/atom <fix_property_atom>` command can be used.  Or an
+defined by the :doc:`fix property/atom <fix_property_atom>` command
-:doc:`atom-style or atomfile-style variable <variable>` can be used; the
+can be used.  Or an :doc:`atom-style or atomfile-style variable
-floating-point value produced by the variable is rounded to an
+<variable>` can be used; the floating-point value produced by the
-integer.  As with bodystyle *molecule*\ , each set of atoms in the fix
+variable is rounded to an integer.  As with bodystyle *molecule*\ ,
-groups with the same integer value is treated as a different rigid
+each set of atoms in the fix groups with the same integer value is
-body.  Since fix property/atom vectors and atom-style variables
+treated as a different rigid body.  Since fix property/atom custom
-produce values for all atoms, you should be careful to use a fix group
+vectors and atom-style variables produce values for all atoms, you
-that only includes atoms you want to be part of rigid bodies.
+should be careful to use a fix group that only includes atoms you want
+to be part of rigid bodies.
 
 .. note::
 

src/RIGID/fix_rigid.cpp

@@ -129,14 +129,10 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
       // determine whether atom-style variable or atom property is used
 
       if (strstr(arg[4],"i_") == arg[4]) {
-        int is_double=0;
+	int flag,cols;
-        int custom_index = atom->find_custom(arg[4]+2,is_double);
+        int custom_index = atom->find_custom(arg[4]+2,flag,cols);
-        if (custom_index == -1)
+	if (custom_index < 0 || !flag || cols)
-          error->all(FLERR,"Fix rigid custom requires "
+          error->all(FLERR,"Fix rigid custom requires custom integer vector");
-                     "previously defined property/atom");
-        else if (is_double)
-          error->all(FLERR,"Fix rigid custom requires "
-                     "integer-valued property/atom");
         int minval = INT_MAX;
         int *value = atom->ivector[custom_index];
         for (i = 0; i < nlocal; i++)

src/RIGID/fix_rigid_small.cpp

@@ -113,15 +113,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
       // determine whether atom-style variable or atom property is used
 
       if (strstr(arg[4],"i_") == arg[4]) {
-        int is_double=0;
+	int flag,cols;
-        int custom_index = atom->find_custom(arg[4]+2,is_double);
+        int custom_index = atom->find_custom(arg[4]+2,flag,cols);
-        if (custom_index == -1)
+	if (custom_index < 0 || !flag || cols)
-          error->all(FLERR,"Fix rigid/small custom requires "
+          error->all(FLERR,"Fix rigid custom requires custom integer vector");
-                     "previously defined property/atom");
-        else if (is_double)
-          error->all(FLERR,"Fix rigid/small custom requires "
-                     "integer-valued property/atom");
-
         int minval = INT_MAX;
         int *value = atom->ivector[custom_index];
         for (i = 0; i < nlocal; i++)

src/USER-REACTION/fix_bond_react.cpp

@@ -683,8 +683,8 @@ void FixBondReact::post_constructor()
       // initialize per-atom statted_flags to 1
       // (only if not already initialized by restart)
       if (fix3->restart_reset != 1) {
-        int flag;
+        int flag,cols;
-        int index = atom->find_custom("statted_tags",flag);
+        int index = atom->find_custom("statted_tags",flag,cols);
         int *i_statted_tags = atom->ivector[index];
 
         for (int i = 0; i < atom->nlocal; i++)
@@ -715,8 +715,8 @@ void FixBondReact::post_constructor()
 
       // initialize per-atom statted_tags to 1
       // need to correct for smooth restarts
-      //int flag;
+      //int flag,cols;
-      //int index = atom->find_custom(statted_id,flag);
+      //int index = atom->find_custom(statted_id,flag,cols);
       //int *i_statted_tags = atom->ivector[index];
       //for (int i = 0; i < atom->nlocal; i++)
       //  i_statted_tags[i] = 1;
@@ -1021,8 +1021,8 @@ void FixBondReact::far_partner()
   firstneigh = list->firstneigh;
 
   // per-atom property indicating if in bond/react master group
-  int flag;
+  int flag,cols;
-  int index1 = atom->find_custom("limit_tags",flag);
+  int index1 = atom->find_custom("limit_tags",flag,cols);
   int *i_limit_tags = atom->ivector[index1];
 
   int i,j;
@@ -1108,8 +1108,8 @@ void FixBondReact::close_partner()
   int *mask = atom->mask;
 
   // per-atom property indicating if in bond/react master group
-  int flag;
+  int flag,cols;
-  int index1 = atom->find_custom("limit_tags",flag);
+  int index1 = atom->find_custom("limit_tags",flag,cols);
   int *i_limit_tags = atom->ivector[index1];
 
   // loop over special list
@@ -1377,8 +1377,8 @@ void FixBondReact::make_a_guess()
   int nfirst_neighs = onemol_nxspecial[pion][0];
 
   // per-atom property indicating if in bond/react master group
-  int flag;
+  int flag,cols;
-  int index1 = atom->find_custom("limit_tags",flag);
+  int index1 = atom->find_custom("limit_tags",flag,cols);
   int *i_limit_tags = atom->ivector[index1];
 
   if (status == GUESSFAIL && avail_guesses == 0) {
@@ -2341,17 +2341,17 @@ void FixBondReact::limit_bond(int limit_bond_mode)
   // we must keep our own list of limited atoms
   // this will be a new per-atom property!
 
-  int flag;
+  int flag,cols;
-  int index1 = atom->find_custom("limit_tags",flag);
+  int index1 = atom->find_custom("limit_tags",flag,cols);
   int *i_limit_tags = atom->ivector[index1];
 
   int *i_statted_tags;
   if (stabilization_flag == 1) {
-    int index2 = atom->find_custom(statted_id,flag);
+    int index2 = atom->find_custom(statted_id,flag,cols);
     i_statted_tags = atom->ivector[index2];
   }
 
-  int index3 = atom->find_custom("react_tags",flag);
+  int index3 = atom->find_custom("react_tags",flag,cols);
   int *i_react_tags = atom->ivector[index3];
 
   for (int i = 0; i < temp_limit_num; i++) {
@@ -2374,17 +2374,17 @@ void FixBondReact::unlimit_bond()
   //let's now unlimit in terms of i_limit_tags
   //we just run through all nlocal, looking for > limit_duration
   //then we return i_limit_tag to 0 (which removes from dynamic group)
-  int flag;
+  int flag,cols;
-  int index1 = atom->find_custom("limit_tags",flag);
+  int index1 = atom->find_custom("limit_tags",flag,cols);
   int *i_limit_tags = atom->ivector[index1];
 
   int *i_statted_tags;
   if (stabilization_flag == 1) {
-    int index2 = atom->find_custom(statted_id,flag);
+    int index2 = atom->find_custom(statted_id,flag,cols);
     i_statted_tags = atom->ivector[index2];
   }
 
-  int index3 = atom->find_custom("react_tags",flag);
+  int index3 = atom->find_custom("react_tags",flag,cols);
   int *i_react_tags = atom->ivector[index3];
 
   for (int i = 0; i < atom->nlocal; i++) {

src/USER-VTK/dump_vtk.cpp

@@ -237,9 +237,15 @@ void DumpVTK::init_style()
 
   int icustom;
   for (int i = 0; i < ncustom; i++) {
-    icustom = atom->find_custom(id_custom[i],flag_custom[i]);
+    int flag,cols;
+    icustom = atom->find_custom(id_custom[i],flag,cols);
     if (icustom < 0)
-      error->all(FLERR,"Could not find custom per-atom property ID");
+      error->all(FLERR,"Could not find dump vtk atom property name");
+    custom[i] = icustom;
+    if (!flag && !cols) custom_flag[i] = IVEC;
+    else if (flag && !cols) custom_flag[i] = DVEC;
+    else if (!flag && cols) custom_flag[i] = IARRAY;
+    else if (flag && cols) custom_flag[i] = DARRAY;
   }
 
   // set index and check validity of region
@@ -1511,6 +1517,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
   name[Z] = "z";
 
   // customize by adding to if statement
+  
   int i;
   for (int iarg = 5; iarg < narg; iarg++) {
     i = iarg-5;
@@ -1825,49 +1832,67 @@ int DumpVTK::parse_fields(int narg, char **arg)
       name[ATTRIBUTES+i] = suffix;
       delete [] suffix;
 
-    // custom per-atom floating point value = d_ID
+    // custom per-atom integer value = i_ID or d_ID
+
+    } else if (strncmp(arg[iarg],"i_",2) == 0 ||
+	       strncmp(arg[iarg],"d_",2) == 0) {
+      int which = 0;
+      if (arg[iarg][0] == 'd') which = 1;
 
-    } else if (strncmp(arg[iarg],"d_",2) == 0) {
       pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
-      vtype[ATTRIBUTES+i] = Dump::DOUBLE;
+      if (!which) vtype[ATTRIBUTES+i] = Dump::INT;
+      else vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
       int n = strlen(arg[iarg]);
       char *suffix = new char[n];
       strcpy(suffix,&arg[iarg][2]);
       argindex[ATTRIBUTES+i] = 0;
 
-      int tmp = -1;
+      int flag,cols;
-      n = atom->find_custom(suffix,tmp);
+      n = atom->find_custom(suffix,flag,cols);
-      if (n < 0)
+      if ((!which && (n < 0 || flag || cols)) ||
-        error->all(FLERR,"Could not find custom per-atom property ID");
+	  (which && (n < 0 || !flag || cols)))
+        error->all(FLERR,"Dump vtk per-atom custom vector does not exist");
 
-      if (tmp != 1)
+      field2index[ATTRIBUTES+i] = add_custom(suffix);
-        error->all(FLERR,"Custom per-atom property ID is not floating point");
-
-      field2index[ATTRIBUTES+i] = add_custom(suffix,1);
       name[ATTRIBUTES+i] = suffix;
       delete [] suffix;
 
-    // custom per-atom integer value = i_ID
+    // custom per-atom array = i2_ID or d2_ID, must include bracketed index
+
+    } else if (strncmp(arg[iarg],"i2_",3) == 0 ||
+	       strncmp(arg[iarg],"d2_",3) == 0) {
+      int which = 0;
+      if (arg[iarg][0] == 'd') which = 1;
 
-    } else if (strncmp(arg[iarg],"i_",2) == 0) {
       pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
-      vtype[ATTRIBUTES+i] = Dump::INT;
+      if (!which) vtype[ATTRIBUTES+i] = Dump::INT;
+      else vtype[ATTRIBUTES+i] = Dump::DOUBLE;
 
       int n = strlen(arg[iarg]);
       char *suffix = new char[n];
-      strcpy(suffix,&arg[iarg][2]);
+      strcpy(suffix,&arg[iarg][3]);
-      argindex[ATTRIBUTES+i] = 0;
 
-      int tmp = -1;
+      char *ptr = strchr(suffix,'[');
-      n = atom->find_custom(suffix,tmp);
+      if (ptr) {
-      if (n < 0)
+        if (suffix[strlen(suffix)-1] != ']')
-        error->all(FLERR,"Could not find custom per-atom property ID");
+          error->all(FLERR,"Invalid attribute in dump custom command");
+	suffix[strlen(suffix)-1] = '\0';
+        argindex[ATTRIBUTES+i] = utils::inumeric(FLERR,ptr+1,true,lmp);
+        *ptr = '\0';
+      } else error->all(FLERR,"Dump custom per-atom custom array is not indexed");
 
-      if (tmp != 0)
+      int flag,cols;
-        error->all(FLERR,"Custom per-atom property ID is not integer");
+      n = atom->find_custom(suffix,flag,cols);
+      
+      if ((!which && (n < 0 || flag || !cols)) ||
+	  (which && (n < 0 || !flag || !cols)))
+	error->all(FLERR,"Dump vtk per-atom custom array does not exist");
+      if (argindex[i] <= 0 || argindex[i] > cols)
+        error->all(FLERR,
+                   "Dump vtk per-atom custom array is accessed out-of-range");
 
-      field2index[ATTRIBUTES+i] = add_custom(suffix,0);
+      field2index[i] = add_custom(suffix);
       name[ATTRIBUTES+i] = suffix;
       delete [] suffix;
 
@@ -2006,27 +2031,28 @@ int DumpVTK::add_variable(char *id)
 
 /* ----------------------------------------------------------------------
    add custom atom property to list used by dump
-   return index of where this property is in list
+   return index of where this property is in Atom class custom lists
    if already in list, do not add, just return index, else add to list
 ------------------------------------------------------------------------- */
 
-int DumpVTK::add_custom(char *id, int flag)
+int DumpVTK::add_custom(char *id)
 {
   int icustom;
   for (icustom = 0; icustom < ncustom; icustom++)
-    if ((strcmp(id,id_custom[icustom]) == 0)
+    if (strcmp(id,id_custom[icustom]) == 0) break;
-        && (flag == flag_custom[icustom])) break;
   if (icustom < ncustom) return icustom;
 
   id_custom = (char **)
     memory->srealloc(id_custom,(ncustom+1)*sizeof(char *),"dump:id_custom");
-  flag_custom = (int *)
+
-    memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
+  delete [] custom;
+  custom = new int[ncustom+1];
+  delete [] custom_flag;
+  custom_flag = new int[ncustom+1];
 
   int n = strlen(id) + 1;
   id_custom[ncustom] = new char[n];
   strcpy(id_custom[ncustom],id);
-  flag_custom[ncustom] = flag;
 
   ncustom++;
   return ncustom-1;