git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11507 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MC/fix_bond_break.cpp

@@ -128,13 +128,14 @@ int FixBondBreak::setmask()
 
 void FixBondBreak::init()
 {
-  // require special bonds = 0,1,1
+  // require special bonds = *,1,1
+  // [0] can be anything b/c I,J are removed from each other's special list
+  // [1],[2] must be 1.0 b/c only special lists of I,J are updated when
+  //   bond I-J is broken, not special lists of neighbors of I,J,etc
 
   int flag = 0;
-  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
+  if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) flag = 1;
-      force->special_lj[3] != 1.0) flag = 1;
+  if (force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0) flag = 1;
-  if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
-      force->special_coul[3] != 1.0) flag = 1;
   if (flag) error->all(FLERR,"Fix bond/break requires special_bonds = 0,1,1");
 
   // warn if angles, dihedrals, impropers are being used

src/MC/fix_bond_create.cpp

@@ -180,16 +180,17 @@ void FixBondCreate::init()
   if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
     error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
 
-  // require special bonds = 0,1,1
+  // require special bonds = *,1,1
+  // [0] can be anything b/c duplicate bond is checked for
+  // [1],[2] must be 1 b/c only special lists of I,J are updated when
+  //   bond I-J is created, not special lists of neighbors of I,J,etc
 
-  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 ||
+  if (force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
-      force->special_lj[3] != 1.0)
+    error->all(FLERR,"Fix bond/create requires special_bonds lj = *,1,1");
-    error->all(FLERR,"Fix bond/create requires special_bonds lj = 0,1,1");
 
   if (atom->q_flag)
-    if (force->special_coul[1] != 0.0 || force->special_coul[2] != 1.0 ||
+    if (force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
-        force->special_coul[3] != 1.0)
+      error->all(FLERR,"Fix bond/create requires special_bonds coul = *,1,1");
-      error->all(FLERR,"Fix bond/create requires special_bonds coul = 0,1,1");
 
   // warn if angles, dihedrals, impropers are being used
 
@@ -267,7 +268,7 @@ void FixBondCreate::setup(int vflag)
 
 void FixBondCreate::post_integrate()
 {
-  int i,j,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
+  int i,j,k,m,ii,jj,inum,jnum,itype,jtype,n1,n3,possible;
   double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
   int *ilist,*jlist,*numneigh,**firstneigh;
   tagint *slist;
@@ -309,6 +310,8 @@ void FixBondCreate::post_integrate()
 
   double **x = atom->x;
   tagint *tag = atom->tag;
+  tagint **bond_atom = atom->bond_atom;
+  int *num_bond = atom->num_bond;
   int *mask = atom->mask;
   int *type = atom->type;
 
@@ -345,6 +348,16 @@ void FixBondCreate::post_integrate()
       }
       if (!possible) continue;
 
+      // do not allow a duplicate bond to be created
+      // check existing bonds of both I and J
+
+      for (k = 0; k < num_bond[i]; k++)
+        if (bond_atom[i][k] == tag[j]) possible = 0;
+      if (j < nlocal)
+        for (k = 0; k < num_bond[j]; k++)
+          if (bond_atom[j][k] == tag[i]) possible = 0;
+      if (!possible) continue;
+
       delx = xtmp - x[j][0];
       dely = ytmp - x[j][1];
       delz = ztmp - x[j][2];
@@ -386,8 +399,6 @@ void FixBondCreate::post_integrate()
   // and probability constraint is satisfied
 
   int **bond_type = atom->bond_type;
-  tagint **bond_atom = atom->bond_atom;
-  int *num_bond = atom->num_bond;
   int **nspecial = atom->nspecial;
   tagint **special = atom->special;
   int newton_bond = force->newton_bond;
@@ -437,11 +448,10 @@ void FixBondCreate::post_integrate()
     // increment bondcount, convert atom to new type if limit reached
 
     bondcount[i]++;
-    if (type[i] == iatomtype) {
+    if (type[i] == iatomtype)
       if (bondcount[i] == imaxbond) type[i] = inewtype;
-    } else {
+    else
       if (bondcount[i] == jmaxbond) type[i] = jnewtype;
-    }
 
     // count the created bond once
 

src/fix.h

@@ -196,6 +196,10 @@ class Fix : protected Pointers {
   void v_setup(int);
   void v_tally(int, int *, double, double *);
 
+  inline int sbmask(int j) {
+    return j >> SBBITS & 3;
+  }
+
   // union data struct for packing 32-bit and 64-bit ints into double bufs
   // see atom_vec.h for documentation
 

src/read_data.cpp

@@ -139,10 +139,9 @@ void ReadData::command(int narg, char **arg)
     } else error->all(FLERR,"Illegal read_data command");
   }
 
-
   // perform 1-pass read if no molecular topoogy in file
-  // perform 2-pass read if molecular topology
+  // perform 2-pass read if molecular topology,
-  //   1st pass calculates max topology/atom
+  //   first pass calculates max topology/atom
 
   int atomflag,topoflag;
   int bondflag,angleflag,dihedralflag,improperflag;
@@ -180,7 +179,6 @@ void ReadData::command(int narg, char **arg)
 
       atom->allocate_type_arrays();
       atom->avec->grow(n);
-      n = atom->nmax;
 
       domain->print_box("  ");
       domain->set_initial_box();
@@ -428,16 +426,19 @@ void ReadData::command(int narg, char **arg)
     if (!topoflag) break;
     firstpass = 0;
 
-    // reallocate bond,angle,diehdral,improper arrays via grow(),
+    // reallocate bond,angle,diehdral,improper arrays via grow()
-    // using new bond,angle,dihedral,improper per-atom values from 1st pass
+    // use new bond,angle,dihedral,improper per-atom values from 1st pass
     // should leave other atom arrays unchanged, since already nmax in length
+    // if bonds/etc not in data file, initialize per-atom size 
+    //   with extra settings before grow() of these topology arrays
 
     if (bondflag) {
       memory->destroy(atom->bond_type);
       memory->destroy(atom->bond_atom);
       atom->bond_type = NULL;
       atom->bond_atom = NULL;
-    }
+    } else atom->bond_per_atom = atom->extra_bond_per_atom;
+
     if (angleflag) {
       memory->destroy(atom->angle_type);
       memory->destroy(atom->angle_atom1);
@@ -445,7 +446,8 @@ void ReadData::command(int narg, char **arg)
       memory->destroy(atom->angle_atom3);
       atom->angle_type = NULL;
       atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
-    }
+    } else atom->angle_per_atom = atom->extra_angle_per_atom;
+
     if (dihedralflag) {
       memory->destroy(atom->dihedral_type);
       memory->destroy(atom->dihedral_atom1);
@@ -455,7 +457,8 @@ void ReadData::command(int narg, char **arg)
       atom->dihedral_type = NULL;
       atom->dihedral_atom1 = atom->dihedral_atom2 = 
         atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
-    }
+    } else atom->dihedral_per_atom = atom->extra_dihedral_per_atom;
+
     if (improperflag) {
       memory->destroy(atom->improper_type);
       memory->destroy(atom->improper_atom1);
@@ -465,7 +468,7 @@ void ReadData::command(int narg, char **arg)
       atom->improper_type = NULL;
       atom->improper_atom1 = atom->improper_atom2 = 
         atom->improper_atom3 = atom->improper_atom4 = NULL;
-    }
+    } else atom->improper_per_atom = atom->extra_improper_per_atom;
 
     atom->avec->grow(atom->nmax);
   }