multi-data-file support for bond, angles, diheddral, impropers

src/atom.cpp

@@ -611,6 +611,7 @@ void Atom::set_atomflag_defaults()
   // 3rd customization section: customize by adding new flag
   // identical list as 2nd customization in atom.h
 
+  labelmapflag = 0;
   sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
   peri_flag = electron_flag = 0;
   wavepacket_flag = sph_flag = 0;
@@ -1247,7 +1248,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
 ------------------------------------------------------------------------- */
 
 void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
-                      int type_offset)
+                      int type_offset, int labelflag, int *ilabel)
 {
   int m,tmp,itype,rv;
   tagint atom1,atom2;
@@ -1265,6 +1266,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
       atom1 += id_offset;
       atom2 += id_offset;
     }
+    if (labelflag) itype = ilabel[itype-1];
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1302,7 +1304,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
 ------------------------------------------------------------------------- */
 
 void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
-                       int type_offset)
+                       int type_offset, int labelflag, int *ilabel)
 {
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3;
@@ -1321,6 +1323,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
       atom2 += id_offset;
       atom3 += id_offset;
     }
+    if (labelflag) itype = ilabel[itype-1];
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1374,7 +1377,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
 ------------------------------------------------------------------------- */
 
 void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
-                          int type_offset)
+                          int type_offset, int labelflag, int *ilabel)
 {
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3,atom4;
@@ -1395,6 +1398,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
       atom3 += id_offset;
       atom4 += id_offset;
     }
+    if (labelflag) itype = ilabel[itype-1];
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1465,7 +1469,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
 ------------------------------------------------------------------------- */
 
 void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
-                          int type_offset)
+                          int type_offset, int labelflag, int *ilabel)
 {
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3,atom4;
@@ -1486,6 +1490,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
       atom3 += id_offset;
       atom4 += id_offset;
     }
+    if (labelflag) itype = ilabel[itype-1];
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||

src/atom.h

@@ -166,6 +166,7 @@ class Atom : protected Pointers {
   // most are existence flags for per-atom vectors and arrays
   // 1 if variable is used, 0 if not
 
+  int labelmapflag;              // type labels
   int sphere_flag,ellipsoid_flag,line_flag,tri_flag,body_flag;
   int peri_flag,electron_flag;
   int wavepacket_flag,sph_flag;
@@ -304,10 +305,10 @@ class Atom : protected Pointers {
   void data_atoms(int, char *, tagint, tagint, int, int, double *,
                   int, int *);
   void data_vels(int, char *, tagint);
-  void data_bonds(int, char *, int *, tagint, int);
+  void data_bonds(int, char *, int *, tagint, int, int, int *);
-  void data_angles(int, char *, int *, tagint, int);
+  void data_angles(int, char *, int *, tagint, int, int, int *);
-  void data_dihedrals(int, char *, int *, tagint, int);
+  void data_dihedrals(int, char *, int *, tagint, int, int, int *);
-  void data_impropers(int, char *, int *, tagint, int);
+  void data_impropers(int, char *, int *, tagint, int, int, int *);
   void data_bonus(int, char *, AtomVec *, tagint);
   void data_bodies(int, char *, AtomVec *, tagint);
   void data_fix_compute_variable(int, int);

src/read_data.cpp

@@ -124,7 +124,7 @@ void ReadData::command(int narg, char **arg)
   addflag = NONE;
   coeffflag = 1;
   id_offset = mol_offset = 0;
-  offsetflag = shiftflag = labelflag = 0;
+  offsetflag = shiftflag = settypeflag = labelflag = 0;
   toffset = boffset = aoffset = doffset = ioffset = 0;
   shift[0] = shift[1] = shift[2] = 0.0;
   extra_atom_types = extra_bond_types = extra_angle_types =
@@ -1379,7 +1379,8 @@ void ReadData::bonds(int firstpass)
     nchunk = MIN(nbonds-nread,CHUNK);
     eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
     if (eof) error->all(FLERR,"Unexpected end of data file");
-    atom->data_bonds(nchunk,buffer,count,id_offset,boffset);
+    atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
+                     labelflag,lmap->lmap2lmap.bond);
     nread += nchunk;
   }
 
@@ -1453,7 +1454,8 @@ void ReadData::angles(int firstpass)
     nchunk = MIN(nangles-nread,CHUNK);
     eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
     if (eof) error->all(FLERR,"Unexpected end of data file");
-    atom->data_angles(nchunk,buffer,count,id_offset,aoffset);
+    atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
+                      labelflag,lmap->lmap2lmap.angle);
     nread += nchunk;
   }
 
@@ -1527,7 +1529,8 @@ void ReadData::dihedrals(int firstpass)
     nchunk = MIN(ndihedrals-nread,CHUNK);
     eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
     if (eof) error->all(FLERR,"Unexpected end of data file");
-    atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset);
+    atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
+                         labelflag,lmap->lmap2lmap.dihedral);
     nread += nchunk;
   }
 
@@ -1601,7 +1604,8 @@ void ReadData::impropers(int firstpass)
     nchunk = MIN(nimpropers-nread,CHUNK);
     eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
     if (eof) error->all(FLERR,"Unexpected end of data file");
-    atom->data_impropers(nchunk,buffer,count,id_offset,ioffset);
+    atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
+                         labelflag,lmap->lmap2lmap.improper);
     nread += nchunk;
   }
 
@@ -1789,6 +1793,7 @@ void ReadData::bodies(int firstpass, AtomVec *ptr)
 
 void ReadData::mass()
 {
+  settypeflag = 1;
   char *next;
   char *buf = new char[ntypes*MAXLINE];
 
@@ -1965,11 +1970,13 @@ void ReadData::impropercoeffs(int which)
 
 void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, int mode)
 {
+  if (settypeflag) error->all(FLERR,"Must read Type Labels before any section involving types");
   int n;
   char *next;
   char *buf = new char[myntypes*MAXLINE];
 
   labelflag = 1;
+  atom->labelmapflag = 1;
 
   int eof = comm->read_lines_from_file(fp,myntypes,MAXLINE,buf);
   if (eof) error->all(FLERR,"Unexpected end of data file");
@@ -2158,6 +2165,7 @@ void ReadData::skip_lines(bigint n)
 void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
                             int noffset, int offset, int *ilabel)
 {
+  settypeflag = 1;
   char *ptr;
   if ((ptr = strchr(line,'#'))) *ptr = '\0';
 

src/read_data.h

@@ -67,7 +67,7 @@ class ReadData : protected Pointers {
 
   // optional args
 
-  int addflag,offsetflag,shiftflag,coeffflag,labelflag;
+  int addflag,offsetflag,shiftflag,coeffflag,settypeflag,labelflag;
   tagint addvalue;
   int toffset,boffset,aoffset,doffset,ioffset;
   double shift[3];
@@ -264,6 +264,11 @@ E: Must read Atoms before Bodies
 
 The Atoms section of a data file must come before a Bodies section.
 
+E: Must read Type Labels before any section involving types
+
+All Type Labels sections of a data file must come before any
+section that uses per-type values (Masses, Coeffs, etc.).
+
 E: Must define pair_style before Pair Coeffs
 
 Must use a pair_style command before reading a data file that defines

src/write_data.cpp

@@ -186,7 +186,7 @@ void WriteData::write(const std::string &file)
 
   if (me == 0) {
     header();
-    atom->lmap->write_data(fp); // NOTE: always write for now, for testing
+    if (atom->labelmapflag) atom->lmap->write_data(fp);
     type_arrays();
     if (coeffflag) force_fields();
   }