git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11802 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MC/fix_bond_break.cpp

@@ -104,11 +104,11 @@ FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
   maxbreak = 0;
   broken = NULL;
 
-  maxinfluenced = 0;
-  influenced = NULL;
-  
   // copy = special list for one atom
-  // may contain 1-2 neighs of all 1-3 neighs before dedup() shrinks it
+  // size = ms^2 + ms is sufficient
+  // b/c in rebuild_special() neighs of all 1-2s are added,
+  //   then a dedup(), then neighs of all 1-3s are added, then final dedup()
+  // this means intermediate size cannot exceed ms^2 + ms
 
   int maxspecial = atom->maxspecial;
   copy = new tagint[maxspecial*maxspecial + maxspecial];
@@ -131,7 +131,6 @@ FixBondBreak::~FixBondBreak()
   memory->destroy(finalpartner);
   memory->destroy(distsq);
   memory->destroy(broken);
-  memory->destroy(influenced);
   delete [] copy;
 }
 
@@ -152,6 +151,15 @@ void FixBondBreak::init()
   if (strstr(update->integrate_style,"respa"))
     nlevels_respa = ((Respa *) update->integrate)->nlevels;
 
+  // enable angle/dihedral/improper breaking if any defined
+
+  if (atom->nangles) angleflag = 1;
+  else angleflag = 0;
+  if (atom->ndihedrals) dihedralflag = 1;
+  else dihedralflag = 0;
+  if (atom->nimpropers) improperflag = 1;
+  else improperflag = 0;
+
   if (force->improper) {
     if (force->improper_match("class2") || force->improper_match("ring"))
       error->all(FLERR,"Cannot yet use fix bond/break with this "
@@ -406,37 +414,27 @@ void FixBondBreak::check_ghosts()
      yes if both atom IDs appear in atom's special list
      else no
    if influenced:
-     check for angles/dihedrals/impropers to break due to broken bond
+     check for angles/dihedrals/impropers to break due to specific broken bonds
      rebuild the atom's special list of 1-2,1-3,1-4 neighs
 ------------------------------------------------------------------------- */
 
 void FixBondBreak::update_topology()
 {
-  int i,j,k,n,influence,found;
+  int i,j,k,n,influence,influenced,found;
   tagint id1,id2;
   tagint *slist;
 
-  int angles_allow = atom->avec->angles_allow;
-  int dihedrals_allow = atom->avec->dihedrals_allow;
-  int impropers_allow = atom->avec->impropers_allow;
-
   tagint *tag = atom->tag;
   int **nspecial = atom->nspecial;
   tagint **special = atom->special;
   int nlocal = atom->nlocal;
 
-  if (nlocal > maxinfluenced) {
-    maxinfluenced = atom->nmax;
-    memory->destroy(influenced);
-    memory->create(influenced,maxinfluenced,"bond/break:influenced");
-  }
-
   nangles = 0;
   ndihedrals = 0;
   nimpropers = 0;
 
   for (i = 0; i < nlocal; i++) {
-    influenced[i] = 0;
+    influenced = 0;
     slist = special[i];
 
     for (j = 0; j < nbreak; j++) {
@@ -453,40 +451,100 @@ void FixBondBreak::update_topology()
         if (found == 2) influence = 1;
       }
       if (!influence) continue;
-      influenced[i] = 1;
+      influenced = 1;
 
-      if (angles_allow) break_angles(i,id1,id2);
-      if (dihedrals_allow) break_dihedrals(i,id1,id2);
-      if (impropers_allow) break_impropers(i,id1,id2);
+      if (angleflag) break_angles(i,id1,id2);
+      if (dihedralflag) break_dihedrals(i,id1,id2);
+      if (improperflag) break_impropers(i,id1,id2);
     }
+
+    if (influenced) rebuild_special(i);
   }
   
   int newton_bond = force->newton_bond;
 
   int all;
-  if (angles_allow) {
+  if (angleflag) {
     MPI_Allreduce(&nangles,&all,1,MPI_INT,MPI_SUM,world);
     if (!newton_bond) all /= 3;
     atom->nangles -= all;
   }
-  if (dihedrals_allow) {
+  if (dihedralflag) {
     MPI_Allreduce(&ndihedrals,&all,1,MPI_INT,MPI_SUM,world);
     if (!newton_bond) all /= 4;
     atom->ndihedrals -= all;
   }
-  if (impropers_allow) {
+  if (improperflag) {
     MPI_Allreduce(&nimpropers,&all,1,MPI_INT,MPI_SUM,world);
     if (!newton_bond) all /= 4;
     atom->nimpropers -= all;
   }
+}
+
+/* ----------------------------------------------------------------------
+   re-build special list of atom M
+   does not affect 1-2 neighs (already include effects of new bond)
+   affects 1-3 and 1-4 neighs due to other atom's augmented 1-2 neighs
+------------------------------------------------------------------------- */
+
+void FixBondBreak::rebuild_special(int m)
+{
+  int i,j,n,n1,cn1,cn2,cn3;
+  tagint *slist;
+
+  tagint *tag = atom->tag;
+  int **nspecial = atom->nspecial;
+  tagint **special = atom->special;
+
+  // existing 1-2 neighs of atom M
+
+  slist = special[m];
+  n1 = nspecial[m][0];
+  cn1 = 0;
+  for (i = 0; i < n1; i++)
+    copy[cn1++] = slist[i];
+
+  // new 1-3 neighs of atom M, based on 1-2 neighs of 1-2 neighs
+  // exclude self
+  // remove duplicates after adding all possible 1-3 neighs
+
+  cn2 = cn1;
+  for (i = 0; i < cn1; i++) {
+    n = atom->map(copy[i]);
+    slist = special[n];
+    n1 = nspecial[n][0];
+    for (j = 0; j < n1; j++)
+      if (slist[j] != tag[m]) copy[cn2++] = slist[j];
+  }
+
+  cn2 = dedup(cn1,cn2,copy);
+
+  // new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
+  // exclude self
+  // remove duplicates after adding all possible 1-4 neighs
 
-  for (i = 0; i < nlocal; i++)
-    if (influenced[i]) rebuild_special(i);
+  cn3 = cn2;
+  for (i = cn1; i < cn2; i++) {
+    n = atom->map(copy[i]);
+    slist = special[n];
+    n1 = nspecial[n][0];
+    for (j = 0; j < n1; j++)
+      if (slist[j] != tag[m]) copy[cn3++] = slist[j];
+  }
+
+  cn3 = dedup(cn2,cn3,copy);
+
+  // store new special list with atom M
+
+  nspecial[m][0] = cn1;
+  nspecial[m][1] = cn2;
+  nspecial[m][2] = cn3;
+  memcpy(special[m],copy,cn3*sizeof(int));
 }
 
 /* ----------------------------------------------------------------------
    break any angles owned by atom M that include atom IDs 1 and 2
-   angle is broken if ID1-ID2 is one of 2 bonds in linear angle
+   angle is broken if ID1-ID2 is one of 2 bonds in angle (I-J,J-K)
 ------------------------------------------------------------------------- */
 
 void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
@@ -523,8 +581,8 @@ void FixBondBreak::break_angles(int m, tagint id1, tagint id2)
 }
 
 /* ----------------------------------------------------------------------
-   break any dihedrals owned by atom M that include atom IDs 1,2,3
-   dihedral is broken if ID1-ID2 is one of 3 bonds in linear dihedral
+   break any dihedrals owned by atom M that include atom IDs 1 and 2
+   dihedral is broken if ID1-ID2 is one of 3 bonds in dihedral (I-J,J-K.K-L)
 ------------------------------------------------------------------------- */
 
 void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
@@ -565,7 +623,7 @@ void FixBondBreak::break_dihedrals(int m, tagint id1, tagint id2)
 }
 
 /* ----------------------------------------------------------------------
-   break any impropers owned by atom M that include atom IDs 1,2,3
+   break any impropers owned by atom M that include atom IDs 1 and 2
    improper is broken if ID1-ID2 is one of 3 bonds in improper (I-J,I-K,I-L)
 ------------------------------------------------------------------------- */
 
@@ -606,68 +664,6 @@ void FixBondBreak::break_impropers(int m, tagint id1, tagint id2)
   atom->num_improper[m] = num_improper;
 }
 
-
-/* ----------------------------------------------------------------------
-   re-build special list of atom M due to bond ID1-ID2 being formed
-   does not affect 1-2 neighs (already include effects of new bond)
-   may affect 1-3 and 1-4 bonds
-------------------------------------------------------------------------- */
-
-void FixBondBreak::rebuild_special(int m)
-{
-  int i,j,n,n1,cn1,cn2,cn3;
-  tagint *slist;
-
-  tagint *tag = atom->tag;
-  int **nspecial = atom->nspecial;
-  tagint **special = atom->special;
-
-  // new 1-2 neighs of atom M
-
-  slist = special[m];
-  n1 = nspecial[m][0];
-  cn1 = 0;
-  for (i = 0; i < n1; i++)
-    copy[cn1++] = slist[i];
-
-  // new 1-3 neighs of atom M, based on 1-2 neighs of 1-2 neighs
-  // exclude self
-  // remove duplicates after adding all possible 1-3 neighs
-
-  cn2 = cn1;
-  for (i = 0; i < cn1; i++) {
-    n = atom->map(copy[i]);
-    slist = special[n];
-    n1 = nspecial[n][0];
-    for (j = 0; j < n1; j++)
-      if (slist[j] != tag[m]) copy[cn2++] = slist[j];
-  }
-
-  cn2 = dedup(cn1,cn2,copy);
-
-  // new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
-  // exclude self
-  // remove duplicates after adding all possible 1-4 neighs
-
-  cn3 = cn2;
-  for (i = cn1; i < cn2; i++) {
-    n = atom->map(copy[i]);
-    slist = special[n];
-    n1 = nspecial[n][0];
-    for (j = 0; j < n1; j++)
-      if (slist[j] != tag[m]) copy[cn3++] = slist[j];
-  }
-
-  cn3 = dedup(cn2,cn3,copy);
-
-  // store new special list with atom M
-
-  nspecial[m][0] = cn1;
-  nspecial[m][1] = cn2;
-  nspecial[m][2] = cn3;
-  memcpy(special[m],copy,cn3*sizeof(int));
-}
-
 /* ----------------------------------------------------------------------
    remove all ID duplicates in copy from Nstart:Nstop-1
    compare to all previous values in copy
@@ -853,6 +849,5 @@ double FixBondBreak::memory_usage()
   int nmax = atom->nmax;
   double bytes = 2*nmax * sizeof(tagint);
   bytes += nmax * sizeof(double);
-  bytes += maxinfluenced * sizeof(int);
   return bytes;
 }

src/MC/fix_bond_break.h

@@ -44,6 +44,7 @@ class FixBondBreak : public Fix {
   int me,nprocs;
   int btype,seed;
   double cutoff,cutsq,fraction;
+  int angleflag,dihedralflag,improperflag;
   tagint lastcheck;
 
   int breakcount,breakcounttotal;
@@ -54,8 +55,6 @@ class FixBondBreak : public Fix {
   int nbreak,maxbreak;
   tagint **broken;
 
-  int maxinfluenced;
-  int *influenced;
   tagint *copy;
 
   class RanMars *random;