git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13008 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute.cpp

@@ -68,6 +68,7 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = 0;
+  size_vector_variable = size_array_rows_variable = 0;
 
   tempflag = pressflag = peflag = 0;
   pressatomflag = peatomflag = 0;

src/compute.h

@@ -39,6 +39,8 @@ class Compute : protected Pointers {
   int size_vector;          // length of global vector
   int size_array_rows;      // rows in global array
   int size_array_cols;      // columns in global array
+  int size_vector_variable;      // 1 if vec length is unknown in advance
+  int size_array_rows_variable;  // 1 if array rows is unknown in advance
 
   int peratom_flag;         // 0/1 if compute_peratom() function exists
   int size_peratom_cols;    // 0 = vector, N = columns in peratom array

src/domain.cpp

@@ -471,7 +471,7 @@ void Domain::reset_box()
    MAX is important since coord - prd < lo can happen when coord = hi
    if fix deform, remap velocity of fix group atoms by box edge velocities
    for triclinic, atoms must be in lamda coords (0-1) before pbc is called
-   image = 10 bits for each dimension
+   image = 10 or 20 bits for each dimension depending on sizeof(imageint)
    increment/decrement in wrap-around fashion
 ------------------------------------------------------------------------- */
 

src/fix.cpp

@@ -69,7 +69,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = 0;
-  size_array_rows_variable = 0;
+  size_vector_variable = size_array_rows_variable = 0;
 
   comm_forward = comm_reverse = comm_border = 0;
   restart_reset = 0;

src/fix.h

@@ -57,7 +57,8 @@ class Fix : protected Pointers {
   int size_vector;               // length of global vector
   int size_array_rows;           // rows in global array
   int size_array_cols;           // columns in global array
-  int size_array_rows_variable;  // 1 if row count is unknown in advance
+  int size_vector_variable;      // 1 if vec length is unknown in advance
+  int size_array_rows_variable;  // 1 if array rows is unknown in advance
   int global_freq;               // frequency s/v data is available at
 
   int peratom_flag;              // 0/1 if per-atom data is stored

src/thermo.cpp

@@ -860,14 +860,17 @@ void Thermo::parse_fields(char *str)
         if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
           if (modify->compute[n]->vector_flag == 0)
             error->all(FLERR,"Thermo compute does not compute vector");
-          if (argindex1[nfield] > modify->compute[n]->size_vector)
+          if (argindex1[nfield] > modify->compute[n]->size_vector &&
+              modify->compute[n]->size_vector_variable == 0)
             error->all(FLERR,"Thermo compute vector is accessed out-of-range");
         }
         if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
           if (modify->compute[n]->array_flag == 0)
             error->all(FLERR,"Thermo compute does not compute array");
-          if (argindex1[nfield] > modify->compute[n]->size_array_rows ||
+          if (argindex1[nfield] > modify->compute[n]->size_array_rows &&
-              argindex2[nfield] > modify->compute[n]->size_array_cols)
+              modify->compute[n]->size_array_rows_variable == 0)
+            error->all(FLERR,"Thermo compute array is accessed out-of-range");
+          if (argindex2[nfield] > modify->compute[n]->size_array_cols)
             error->all(FLERR,"Thermo compute array is accessed out-of-range");
         }
 
@@ -887,16 +890,16 @@ void Thermo::parse_fields(char *str)
         if (argindex1[nfield] > 0 && argindex2[nfield] == 0) {
           if (modify->fix[n]->vector_flag == 0)
             error->all(FLERR,"Thermo fix does not compute vector");
-          if (argindex1[nfield] > modify->fix[n]->size_vector)
+          if (argindex1[nfield] > modify->fix[n]->size_vector && 
+              modify->fix[n]->size_vector_variable == 0)
             error->all(FLERR,"Thermo fix vector is accessed out-of-range");
         }
         if (argindex1[nfield] > 0 && argindex2[nfield] > 0) {
           if (modify->fix[n]->array_flag == 0)
             error->all(FLERR,"Thermo fix does not compute array");
-          if (argindex1[nfield] > modify->fix[n]->size_array_rows) {
+          if (argindex1[nfield] > modify->fix[n]->size_array_rows &&
-            if (modify->fix[n]->size_array_rows_variable == 0)
+              modify->fix[n]->size_array_rows_variable == 0)
-              error->all(FLERR,"Thermo fix array is accessed out-of-range");
+            error->all(FLERR,"Thermo fix array is accessed out-of-range");
-          }
           if (argindex2[nfield] > modify->fix[n]->size_array_cols)
             error->all(FLERR,"Thermo fix array is accessed out-of-range");
         }
@@ -1422,18 +1425,24 @@ void Thermo::compute_compute()
   int m = field2index[ifield];
   Compute *compute = computes[m];
 
+  // check for out-of-range access if vector/array is variable length
+
   if (compute_which[m] == SCALAR) {
     dvalue = compute->scalar;
     if (normflag && compute->extscalar) dvalue /= natoms;
   } else if (compute_which[m] == VECTOR) {
-    dvalue = compute->vector[argindex1[ifield]-1];
+    if (compute->size_vector_variable && argindex1[ifield] > 
+        compute->size_vector) dvalue = 0.0;
+    else dvalue = compute->vector[argindex1[ifield]-1];
     if (normflag) {
       if (compute->extvector == 0) return;
       else if (compute->extvector == 1) dvalue /= natoms;
       else if (compute->extlist[argindex1[ifield]-1]) dvalue /= natoms;
     }
   } else {
-    dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
+    if (compute->size_array_rows_variable && argindex1[ifield] > 
+        compute->size_array_rows) dvalue = 0.0;
+    else dvalue = compute->array[argindex1[ifield]-1][argindex2[ifield]-1];
     if (normflag && compute->extarray) dvalue /= natoms;
   }
 }

src/variable.cpp

@@ -1081,7 +1081,8 @@ double Variable::evaluate(char *str, Tree **tree)
 
         } else if (nbracket == 1 && compute->vector_flag) {
 
-          if (index1 > compute->size_vector)
+          if (index1 > compute->size_vector &&
+              compute->size_vector_variable == 0)
             error->all(FLERR,"Variable formula compute vector "
                        "is accessed out-of-range");
           if (update->whichflag == 0) {
@@ -1093,7 +1094,9 @@ double Variable::evaluate(char *str, Tree **tree)
             compute->invoked_flag |= INVOKED_VECTOR;
           }
 
-          value1 = compute->vector[index1-1];
+          if (compute->size_vector_variable && 
+              index1 > compute->size_vector) value1 = 0.0;
+          else value1 = compute->vector[index1-1];
           if (tree) {
             Tree *newtree = new Tree();
             newtree->type = VALUE;
@@ -1107,7 +1110,8 @@ double Variable::evaluate(char *str, Tree **tree)
 
         } else if (nbracket == 2 && compute->array_flag) {
 
-          if (index1 > compute->size_array_rows)
+          if (index1 > compute->size_array_rows &&
+              compute->size_array_rows_variable == 0)
             error->all(FLERR,"Variable formula compute array "
                        "is accessed out-of-range");
           if (index2 > compute->size_array_cols)
@@ -1122,7 +1126,9 @@ double Variable::evaluate(char *str, Tree **tree)
             compute->invoked_flag |= INVOKED_ARRAY;
           }
 
-          value1 = compute->array[index1-1][index2-1];
+          if (compute->size_array_rows_variable && 
+              index1 > compute->size_array_rows) value1 = 0.0;
+          else value1 = compute->array[index1-1][index2-1];
           if (tree) {
             Tree *newtree = new Tree();
             newtree->type = VALUE;
@@ -1295,12 +1301,13 @@ double Variable::evaluate(char *str, Tree **tree)
 
         } else if (nbracket == 1 && fix->vector_flag) {
 
-          if (index1 > fix->size_vector)
+          if (index1 > fix->size_vector &&
-            error->all(FLERR,
+              fix->size_vector_variable == 0)
-                       "Variable formula fix vector is accessed out-of-range");
+            error->all(FLERR,"Variable formula fix vector is "
+                       "accessed out-of-range");
           if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
             error->all(FLERR,"Fix in variable not computed at compatible time");
-
+          
           value1 = fix->compute_vector(index1-1);
           if (tree) {
             Tree *newtree = new Tree();
@@ -1315,11 +1322,10 @@ double Variable::evaluate(char *str, Tree **tree)
 
         } else if (nbracket == 2 && fix->array_flag) {
 
-          if (index1 > fix->size_array_rows) {
+          if (index1 > fix->size_array_rows &&
-            if (fix->size_array_rows_variable == 0)
+              fix->size_array_rows_variable == 0)
-              error->all(FLERR,
+            error->all(FLERR,
-                         "Variable formula fix array is accessed out-of-range");
+                       "Variable formula fix array is accessed out-of-range");
-          }
           if (index2 > fix->size_array_cols)
             error->all(FLERR,
                        "Variable formula fix array is accessed out-of-range");