Modified data_bonds_post() and calling structure

examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1

@@ -32,7 +32,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.4

@@ -32,7 +32,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1

@@ -32,7 +32,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.4

@@ -32,7 +32,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.1

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/log.27May21.duplex1.g++.4

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.1

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/log.27May21.duplex2.g++.4

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.1

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/log.27May21.duplex3.g++.4

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   10 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   8 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++1

@@ -36,7 +36,6 @@ Reading data file ...
   2 = max bonds/atom
   26 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   24 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.4type.g++4

@@ -36,7 +36,6 @@ Reading data file ...
   2 = max bonds/atom
   26 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   24 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++1

@@ -36,7 +36,6 @@ Reading data file ...
   2 = max bonds/atom
   26 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   24 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/log.27May21.duplex4.8type.g++4

@@ -36,7 +36,6 @@ Reading data file ...
   2 = max bonds/atom
   26 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   24 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.1

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/log.27May21.duplex2.g++.4

@@ -33,7 +33,6 @@ Reading data file ...
   2 = max bonds/atom
   16 ellipsoids
   reading bonds ...
-Setting oxDNA 3'->5' bond directionality ...
   13 bonds
 Finding 1-2 1-3 1-4 neighbors ...
   special bond factors lj:    0        0        0       

src/CG-DNA/atom_vec_oxdna.cpp

@@ -66,7 +66,7 @@ void AtomVecOxdna::grow_pointers()
 }
 
 /* ----------------------------------------------------------------------
-   initialize atom quantity
+   initialize atom quantity 5' partner
 ------------------------------------------------------------------------- */
 
 void AtomVecOxdna::data_atom_post(int ilocal)
@@ -80,45 +80,17 @@ void AtomVecOxdna::data_atom_post(int ilocal)
    store 5' partner to inform 3'->5' bond directionality 
 ------------------------------------------------------------------------- */
 
-void AtomVecOxdna::data_bonds_post(int n, char *buf, tagint id_offset)
+void AtomVecOxdna::data_bonds_post(int m, int num_bond, tagint atom1,
+                                       tagint atom2, tagint id_offset)
 {
-
- int m,tmp,itype,rv;
-  tagint atom1,atom2;
-  char *next;
-
   tagint *id5p = atom->id5p;
 
-  if (comm->me == 0) utils::logmesg(lmp,"Setting oxDNA 3'->5' bond directionality ...\n");
+  if (id_offset) {
+    atom1 += id_offset;
+    atom2 += id_offset;
+  }
 
-  for (int i = 0; i < n; i++) {
+  if ((m = atom->map(atom1)) >= 0) {
-
+      id5p[m] = atom2;
-    next = strchr(buf,'\n');
-    *next = '\0';
-    rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
-                &tmp,&itype,&atom1,&atom2);
-
-    if (id_offset) {
-      atom1 += id_offset;
-      atom2 += id_offset;
-    }
-
-    if ((m = atom->map(atom1)) >= 0) {
-        id5p[m] = atom2;
-    }
-
-    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

@@ -30,8 +30,7 @@ class AtomVecOxdna : public AtomVec {
   ~AtomVecOxdna();
 
   void grow_pointers();
-  virtual void data_bonds_post(int, char *, tagint);
+  virtual void data_bonds_post(int, int, tagint, tagint, tagint);
-  virtual void data_bonds_post2(int, int, tagint, tagint, tagint);
   void data_atom_post(int);
 
  private:

src/atom.cpp

@@ -1288,7 +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);
+        avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
       }
     }
     if (newton_bond == 0) {
@@ -1298,6 +1298,7 @@ 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]] = atom1;
           num_bond[m]++;
+          avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
         }
       }
     }

src/atom_vec.h

@@ -129,8 +129,7 @@ class AtomVec : protected Pointers {
   virtual void data_atom_bonus(int, char **) {}
   virtual void data_body(int, int, int, int *, double *) {}
 
-  virtual void data_bonds_post(int, char *, tagint) {}
+  virtual void data_bonds_post(int, int , tagint, tagint, 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

@@ -442,11 +442,11 @@ void AtomVecHybrid::data_atom_post(int 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)
+void AtomVecHybrid::data_bonds_post(int m, int num_bond, tagint atom1,
+                                        tagint atom2, tagint id_offset)
 {                     
-
+  for (int k = 0; k < nstyles; k++)
-printf("CALLED FROM ATOM_VEC_HYBRID\n");
+    styles[k]->data_bonds_post(m, num_bond, atom1, atom2, id_offset);
-
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec_hybrid.h

@@ -56,7 +56,7 @@ class AtomVecHybrid : public AtomVec {
   void create_atom_post(int);
   void data_atom_post(int);
 
-  virtual void data_bonds_post2(int, int, tagint, tagint, tagint);
+  virtual void data_bonds_post(int, int, tagint, tagint, tagint);
 
   void pack_data_pre(int);
   void pack_data_post(int);

src/read_data.cpp

@@ -1342,7 +1342,6 @@ void ReadData::bonds(int firstpass)
     if (eof) error->all(FLERR,"Unexpected end of data file");
     strcpy(buffer_post,buffer);
     atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
-    if (!firstpass) avec->data_bonds_post(nchunk,buffer_post,id_offset);
     nread += nchunk;
   }