Merge pull request #1067 from jrgissing/bond/react-better-template-checks

Bond/react: better template validity checks

doc/src/fix_bond_react.txt

@@ -125,13 +125,13 @@ template. If both these conditions are met, the reaction site is
 modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
-First, a pair of atoms within the specified react-group-ID of type
-typei and typej must separated by a distance between {Rmin} and
+First, a pair of atoms I,J within the specified react-group-ID of type
+itype and jtype must separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
 identified: if the bonding atoms in the pre-reacted template are not
 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
 its bonding partner; otherwise, the farthest potential partner is
-chosen. Then, if both an atomi and atomj have each other as their
+chosen. Then, if both an atom I and atom J have each other as their
 nearest bonding partners, these two atoms are identified as the
 bonding atom pair of the reaction site. Once this unique bonding atom
 pair is identified for each reaction, there could two or more
@@ -323,7 +323,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
 
 [Default:]
 
-The option defaults are stabilization = no, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
 
 :line
 

src/USER-MISC/fix_bond_react.cpp

@@ -1063,8 +1063,8 @@ void FixBondReact::superimpose_algorithm()
         hang_catch++;
         // let's go ahead and catch the simplest of hangs
         //if (hang_catch > onemol->natoms*4)
-        if (hang_catch > atom->nlocal*3) {
-          error->all(FLERR,"Excessive iteration of superimpose algorithm");
+        if (hang_catch > atom->nlocal*30) {
+          error->one(FLERR,"Excessive iteration of superimpose algorithm");
         }
       }
     }
@@ -1554,6 +1554,40 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
       error->one(FLERR,"Atom affected by reaction too close to template edge");
   }
 
+  // additionally, if a bond changes type, but neither involved atom is landlocked, bad
+  // would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
+  for (int i = 0; i < twomol->natoms; i++) {
+    if (landlocked_atoms[i][myrxn] == 0) {
+      int twomol_atomi = i+1;
+      for (int j = 0; j < twomol->num_bond[i]; j++) {
+        int twomol_atomj = twomol->bond_atom[i][j];
+        if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
+          int onemol_atomi = equivalences[i][1][myrxn];
+          int onemol_batom;
+          for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
+            onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
+            if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
+              if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
+                error->one(FLERR,"Bond type affected by reaction too close to template edge");
+              }
+            }
+          }
+          if (newton_bond) {
+            int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
+            for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
+              onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
+              if (onemol_batom == equivalences[i][1][myrxn]) {
+                if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
+                  error->one(FLERR,"Bond type affected by reaction too close to template edge");
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+
   // also, if atoms change number of bonds, but aren't landlocked, that could be bad
   if (me == 0)
     for (int i = 0; i < twomol->natoms; i++) {
@@ -2067,7 +2101,7 @@ void FixBondReact::update_everything()
                   nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
                   nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
                 }
-                for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+                for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) {
                   special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
                 }
                 special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];