Added data_bonds_post2() method for testing purposes

src/CG-DNA/atom_vec_oxdna.cpp

@@ -101,3 +101,15 @@ void AtomVecOxdna::data_bonds_post(int n, char *buf, tagint id_offset)
     buf = next + 1;
   }
 }
+
+/* ----------------------------------------------------------------------
+   process bond information as per data file
+   store 5' partner to inform 3'->5' bond directionality 
+------------------------------------------------------------------------- */
+
+void AtomVecOxdna::data_bonds_post2(int m, int num_bond, tagint atom1, tagint atom2, tagint id_offset)
+{
+
+printf("CALLED FROM ATOM_VEC_OXDNA\n");
+
+}

src/CG-DNA/atom_vec_oxdna.h

@@ -32,6 +32,7 @@ class AtomVecOxdna : public AtomVec {
 
   void grow_pointers();
   virtual void data_bonds_post(int, char *, tagint);
+  virtual void data_bonds_post2(int, int, tagint, tagint, tagint);
 
  private:
   tagint *id5p;

src/atom.cpp

@@ -1288,6 +1288,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
         bond_type[m][num_bond[m]] = itype;
         bond_atom[m][num_bond[m]] = atom2;
         num_bond[m]++;
+        avec->data_bonds_post2(m, num_bond[m], atom1, atom2, id_offset);
       }
     }
     if (newton_bond == 0) {

src/atom_vec.h

@@ -130,6 +130,7 @@ class AtomVec : protected Pointers {
   virtual void data_body(int, int, int, int *, double *) {}
 
   virtual void data_bonds_post(int, char *, tagint) {}
+  virtual void data_bonds_post2(int, int , tagint, tagint, tagint) {}
 
   virtual void pack_data(double **);
   virtual void write_data(FILE *, int, double **);

src/atom_vec_hybrid.cpp

@@ -438,6 +438,17 @@ void AtomVecHybrid::data_atom_post(int ilocal)
     styles[k]->data_atom_post(ilocal);
 }
 
+/* ----------------------------------------------------------------------
+   modify what AtomVec::data_bonds() just unpacked
+   or initialize other bond quantities
+------------------------------------------------------------------------- */
+void AtomVecHybrid::data_bonds_post2(int m, int num_bond, tagint atom1, tagint atom2, tagint id_offset)
+{                     
+
+printf("CALLED FROM ATOM_VEC_HYBRID\n");
+
+}
+
 /* ----------------------------------------------------------------------
    modify values for AtomVec::pack_data() to pack
 ------------------------------------------------------------------------- */

src/atom_vec_hybrid.h

@@ -55,6 +55,9 @@ class AtomVecHybrid : public AtomVec {
   void unpack_restart_init(int);
   void create_atom_post(int);
   void data_atom_post(int);
+
+  virtual void data_bonds_post2(int, int, tagint, tagint, tagint);
+
   void pack_data_pre(int);
   void pack_data_post(int);