git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10328 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/force.cpp

@@ -655,22 +655,22 @@ void Force::set_special(int narg, char **arg)
    compute bounds implied by numeric str with a possible wildcard asterik
    1 = lower bound, nmax = upper bound
    5 possibilities:
-     (1) i = i to i, (2) * = 1 to nmax,
+     (1) i = i to i, (2) * = nmin to nmax,
-     (3) i* = i to nmax, (4) *j = 1 to j, (5) i*j = i to j
+     (3) i* = i to nmax, (4) *j = nmin to j, (5) i*j = i to j
    return nlo,nhi
 ------------------------------------------------------------------------- */
 
-void Force::bounds(char *str, int nmax, int &nlo, int &nhi)
+void Force::bounds(char *str, int nmax, int &nlo, int &nhi, int nmin)
 {
   char *ptr = strchr(str,'*');
 
   if (ptr == NULL) {
     nlo = nhi = atoi(str);
   } else if (strlen(str) == 1) {
-    nlo = 1;
+    nlo = nmin;
     nhi = nmax;
   } else if (ptr == str) {
-    nlo = 1;
+    nlo = nmin;
     nhi = atoi(ptr+1);
   } else if (strlen(ptr+1) == 0) {
     nlo = atoi(str);
@@ -680,7 +680,8 @@ void Force::bounds(char *str, int nmax, int &nlo, int &nhi)
     nhi = atoi(ptr+1);
   }
 
-  if (nlo < 1 || nhi > nmax) error->all(FLERR,"Numeric index is out of bounds");
+  if (nlo < nmin || nhi > nmax) 
+    error->all(FLERR,"Numeric index is out of bounds");
 }
 
 /* ----------------------------------------------------------------------

src/force.h

@@ -99,7 +99,7 @@ class Force : protected Pointers {
   class KSpace *kspace_match(const char *, int);
 
   void set_special(int, char **);
-  void bounds(char *, int, int &, int &);
+  void bounds(char *, int, int &, int &, int nmin=1);
   double numeric(const char *, int, char *);
   int inumeric(const char *, int, char *);
   bigint memory_usage();

src/set.cpp

@@ -67,6 +67,7 @@ void Set::command(int narg, char **arg)
   id = new char[n];
   strcpy(id,arg[1]);
   select = NULL;
+  selection(atom->nlocal);
 
   // loop over keyword/value pairs
   // call appropriate routine to reset attributes
@@ -374,8 +375,7 @@ void Set::selection(int n)
   } else if (style == MOL_SELECT) {
     if (atom->molecule_flag == 0)
       error->all(FLERR,"Cannot use set mol with no molecule IDs defined");
-    if (strcmp(id,"0") == 0) nlo = nhi = 0;
+    else force->bounds(id,BIG,nlo,nhi,0);
-    else force->bounds(id,BIG,nlo,nhi);
 
     int *molecule = atom->molecule;
     for (int i = 0; i < n; i++)
@@ -423,8 +423,6 @@ void Set::set(int keyword)
   AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
   AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
 
-  selection(atom->nlocal);
-
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++) {
     if (!select[i]) continue;
@@ -563,7 +561,6 @@ void Set::setrandom(int keyword)
   AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
   AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
 
-  selection(atom->nlocal);
   RanPark *random = new RanPark(lmp,1);
   double **x = atom->x;
   int seed = ivalue;

src/variable.cpp

@@ -3234,7 +3234,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
     newtree->left = newtree->middle = newtree->right = NULL;
     treestack[ntreestack++] = newtree;
 
-  // special function for file-style or atomfile-stlye variables
+  // special function for file-style or atomfile-style variables
 
   } else if (strcmp(word,"next") == 0) {
     if (narg != 1) 
@@ -3260,16 +3260,14 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
         treestack[ntreestack++] = newtree;
       } else argstack[nargstack++] = value;
 
-    // ATOMFILE has one value per atom, only valid for
+    // ATOMFILE has per-atom values, save values in tree
-    // save values in tree
+    // copy current per-atom values into result so can read next ones
+    // set selfalloc = 1 so result will be deleted by free_tree() after eval
 
     } else if (style[ivar] == ATOMFILE) {
       if (tree == NULL) 
         error->all(FLERR,"Atomfile variable in equal-style variable formula");
 
-      // copy current per-atom values into result so can read next ones
-      // set selfalloc = 1 so will be deleted by free_tree() after eval
-
       double *result;
       memory->create(result,atom->nlocal,"variable:result");
       memcpy(result,reader[ivar]->fix->vstore,atom->nlocal*sizeof(double));