modifications to correctly print modified dihedrals, impropers

src/atom_vec.cpp

@@ -274,7 +274,7 @@ void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index)
    pack dihedral info for data file
 ------------------------------------------------------------------------- */
 
-void AtomVec::pack_dihedral(tagint **buf)
+int AtomVec::pack_dihedral(tagint **buf)
 {
   tagint *tag = atom->tag;
   int *num_dihedral = atom->num_dihedral;
@@ -291,25 +291,31 @@ void AtomVec::pack_dihedral(tagint **buf)
   if (newton_bond) {
     for (i = 0; i < nlocal; i++)
       for (j = 0; j < num_dihedral[i]; j++) {
-        buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
+      	if (buf) {
-        buf[m][1] = dihedral_atom1[i][j];
+          buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
-        buf[m][2] = dihedral_atom2[i][j];
+          buf[m][1] = dihedral_atom1[i][j];
-        buf[m][3] = dihedral_atom3[i][j];
+          buf[m][2] = dihedral_atom2[i][j];
-        buf[m][4] = dihedral_atom4[i][j];
+          buf[m][3] = dihedral_atom3[i][j];
+          buf[m][4] = dihedral_atom4[i][j];
+        }
         m++;
       }
   } else {
     for (i = 0; i < nlocal; i++)
       for (j = 0; j < num_dihedral[i]; j++)
         if (tag[i] == dihedral_atom2[i][j]) {
-          buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
+          if (buf) {
-          buf[m][1] = dihedral_atom1[i][j];
+            buf[m][0] = MAX(dihedral_type[i][j],-dihedral_type[i][j]);
-          buf[m][2] = dihedral_atom2[i][j];
+            buf[m][1] = dihedral_atom1[i][j];
-          buf[m][3] = dihedral_atom3[i][j];
+            buf[m][2] = dihedral_atom2[i][j];
-          buf[m][4] = dihedral_atom4[i][j];
+            buf[m][3] = dihedral_atom3[i][j];
+            buf[m][4] = dihedral_atom4[i][j];
+          }
           m++;
         }
   }
+
+  return m;
 }
 
 /* ----------------------------------------------------------------------
@@ -330,7 +336,7 @@ void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index)
    pack improper info for data file
 ------------------------------------------------------------------------- */
 
-void AtomVec::pack_improper(tagint **buf)
+int AtomVec::pack_improper(tagint **buf)
 {
   tagint *tag = atom->tag;
   int *num_improper = atom->num_improper;
@@ -347,25 +353,31 @@ void AtomVec::pack_improper(tagint **buf)
   if (newton_bond) {
     for (i = 0; i < nlocal; i++)
       for (j = 0; j < num_improper[i]; j++) {
-        buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
+        if (buf) {
-        buf[m][1] = improper_atom1[i][j];
+          buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
-        buf[m][2] = improper_atom2[i][j];
+          buf[m][1] = improper_atom1[i][j];
-        buf[m][3] = improper_atom3[i][j];
+          buf[m][2] = improper_atom2[i][j];
-        buf[m][4] = improper_atom4[i][j];
+          buf[m][3] = improper_atom3[i][j];
+          buf[m][4] = improper_atom4[i][j];
+        }
         m++;
       }
   } else {
     for (i = 0; i < nlocal; i++)
       for (j = 0; j < num_improper[i]; j++)
         if (tag[i] == improper_atom2[i][j]) {
-          buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
+          if (buf) {
-          buf[m][1] = improper_atom1[i][j];
+            buf[m][0] = MAX(improper_type[i][j],-improper_type[i][j]);
-          buf[m][2] = improper_atom2[i][j];
+            buf[m][1] = improper_atom1[i][j];
-          buf[m][3] = improper_atom3[i][j];
+            buf[m][2] = improper_atom2[i][j];
-          buf[m][4] = improper_atom4[i][j];
+            buf[m][3] = improper_atom3[i][j];
+            buf[m][4] = improper_atom4[i][j];
+          }
           m++;
         }
   }
+
+  return m;
 }
 
 /* ----------------------------------------------------------------------

src/atom_vec.h

@@ -107,9 +107,9 @@ class AtomVec : protected Pointers {
   void write_bond(FILE *, int, tagint **, int);
   int pack_angle(tagint **);
   void write_angle(FILE *, int, tagint **, int);
-  void pack_dihedral(tagint **);
+  int pack_dihedral(tagint **);
   void write_dihedral(FILE *, int, tagint **, int);
-  void pack_improper(tagint **);
+  int pack_improper(tagint **);
   void write_improper(FILE *, int, tagint **, int);
 
   virtual int property_atom(char *) {return -1;}

src/write_data.cpp

@@ -152,8 +152,8 @@ void WriteData::write(char *file)
   if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
     error->all(FLERR,"Atom count is inconsistent, cannot write data file");
 
-  // sum up bond,angle counts
+  // sum up bond,angle,dihedral,improper counts
-  // may be different than atom->nbonds,nangles if broken/turned-off
+  // may be different than atom->nbonds,nangles, etc. if broken/turned-off
 
   if (atom->molecular == 1 && (atom->nbonds || atom->nbondtypes)) {
     nbonds_local = atom->avec->pack_bond(NULL);
@@ -164,6 +164,16 @@ void WriteData::write(char *file)
     MPI_Allreduce(&nangles_local,&nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
   }
 
+  if (atom->molecular == 1 && (atom->ndihedrals || atom->ndihedraltypes)) {
+    ndihedrals_local = atom->avec->pack_dihedral(NULL);
+    MPI_Allreduce(&ndihedrals_local,&ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
+  }
+
+  if (atom->molecular == 1 && (atom->nimpropers || atom->nimpropertypes)) {
+    nimpropers_local = atom->avec->pack_improper(NULL);
+    MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
+  }
+
   // open data file
 
   if (me == 0) {

src/write_data.h

@@ -38,6 +38,8 @@ class WriteData : protected Pointers {
   FILE *fp;
   bigint nbonds_local,nbonds;
   bigint nangles_local,nangles;
+  bigint ndihedrals_local,ndihedrals;
+  bigint nimpropers_local,nimpropers;
 
   void header();
   void type_arrays();