preempt some read/write data file bugs

currently, require all type labels (for all interactions) to be defined, if any are, when reading data files

doc/src/read_data.rst

@@ -623,20 +623,23 @@ integers (1, not 1.0).
 
 Type labels can be used to make data files more general, by defining
 atom, bond, etc. types in terms of user-provided strings instead of
-numbers.  If a type label section exists for a given interaction, the
-numeric types listed in the *Atoms*, *Bonds*, etc. section are first
-converted into their corresponding type label before being read into
-LAMMPS; type labels cannot be directly substituted for numeric types
-used in data files.  Data files can also be used to populate the
-default label map; if the type label does not already exist, the type
-label is created as a new type and assigned to the default label map.
-The corresponding interaction coefficients listed in the data file are
-associated to this type.  When reading multiple data files, or if the
-default label map already exists, there must be enough space in the
-per-type data arrays to create new types; see the *extra/atom/types*
-keyword for how to reserve extra space for new types.  Note that, in
-this case, the numeric-to-label mapping within a data file does not
-necessary correspond to that of the simulation; the :doc:`write_data <write_data>`
+numbers.  If a type label section exists for any one interaction
+(atom, bond, angle, dihedral or improper), then all types must be
+assigned a type label for all interactions.  All type label sections
+must come before any section that includes types.  The numeric types
+listed in the *Atoms*, *Bonds*, etc. section are first converted into
+their corresponding type label before being read into LAMMPS; type
+labels cannot be directly substituted for numeric types used in data
+files.  Data files assign all types to the default label map; if the
+type label does not already exist, the type label is created as a new
+type and assigned to the default label map.  The corresponding
+interaction coefficients listed in the data file are associated to
+this type.  There must be enough space in the per-type data
+arrays to create new types; see the *extra/atom/types* keyword for how
+to reserve extra space for new types, e.g., when reading multiple data
+files.  Note that, in this case, the numeric-to-label mapping within a
+data file does not necessary correspond to that of the simulation;
+once the default label map is fully defined, the :doc:`write_data <write_data>`
 command can be used to print out the default label map at a given
 point in a simulation.  See the :doc:`labelmap <labelmap>` command for
 more discussion on how to use type label maps.

doc/src/write_data.rst

@@ -108,7 +108,9 @@ from :doc:`fix property/atom <fix_property_atom>`.
 
 The *nolabelmap* keyword requests that the default label map should
 not be written to the data file (see the Type Label sections of
-:doc:`read_data <read_data>` command for details).
+:doc:`read_data <read_data>` command for details). By default, if the
+default label map is fully defined, i.e. every atom, bond, etc. type
+has an associated type label, it is written to the data file.
 
 The *pair* keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value

src/label_map.cpp

@@ -237,12 +237,46 @@ int LabelMap::search(std::string mylabel, std::vector<std::string> labels, int n
   return -1;
 }
 
+/* ----------------------------------------------------------------------
+   check if all types have been assigned a type label
+------------------------------------------------------------------------- */
+
+int LabelMap::is_complete()
+{
+  for (int i = 0; i < natomtypes; i++)
+    if (typelabel[i].empty()) return 0;
+
+  if (force->bond)
+    for (int i = 0; i < nbondtypes; i++)
+      if (btypelabel[i].empty()) return 0;
+
+  if (force->angle)
+    for (int i = 0; i < nangletypes; i++)
+      if (atypelabel[i].empty()) return 0;
+
+  if (force->dihedral)
+    for (int i = 0; i < ndihedraltypes; i++)
+      if (dtypelabel[i].empty()) return 0;
+
+  if (force->improper)
+    for (int i = 0; i < nimpropertypes; i++)
+      if (itypelabel[i].empty()) return 0;
+
+  return 1;
+}
+
 /* ----------------------------------------------------------------------
    proc 0 writes to data file
 ------------------------------------------------------------------------- */
 
 void LabelMap::write_data(FILE *fp)
 {
+  if (!is_complete()) {
+    error->warning(FLERR,"Default label map is incomplete. "
+                   "Assign all type labels to write to data file.");
+    return;
+  }
+
   fmt::print(fp,"\nAtom Type Labels\n\n");
   for (int i = 0; i < natomtypes; i++)
     fmt::print(fp,"{} {}\n",i+1,typelabel[i]);

src/label_map.h

@@ -48,6 +48,7 @@ class LabelMap : protected Pointers {
    int find_or_create(std::string, std::vector<std::string> &, int); // look up type or create new type
    int find(std::string, int);                                       // find numeric type of type label
    int search(std::string, std::vector<std::string>, int);           // look up type index
+   int is_complete();                                                // check if all types are assigned
 
    // input/output for atom class label map
 

src/read_data.cpp

@@ -1279,6 +1279,9 @@ void ReadData::atoms()
     nchunk = MIN(natoms-nread,CHUNK);
     eof = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
     if (eof) error->all(FLERR,"Unexpected end of data file");
+    if (labelflag && !lmap->is_complete())
+      error->all(FLERR,"Label map is incomplete. "
+                 "All types must be assigned a type label.");
     atom->data_atoms(nchunk,buffer,id_offset,mol_offset,toffset,
                      shiftflag,shift,labelflag,lmap->lmap2lmap.atom);
     nread += nchunk;
@@ -1378,6 +1381,9 @@ 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");
+    if (labelflag && !lmap->is_complete())
+      error->all(FLERR,"Label map is incomplete. "
+                 "All types must be assigned a type label.");
     atom->data_bonds(nchunk,buffer,count,id_offset,boffset,
                      labelflag,lmap->lmap2lmap.bond);
     nread += nchunk;
@@ -1453,6 +1459,9 @@ 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");
+    if (labelflag && !lmap->is_complete())
+      error->all(FLERR,"Label map is incomplete. "
+                 "All types must be assigned a type label.");
     atom->data_angles(nchunk,buffer,count,id_offset,aoffset,
                       labelflag,lmap->lmap2lmap.angle);
     nread += nchunk;
@@ -1528,6 +1537,9 @@ 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");
+    if (labelflag && !lmap->is_complete())
+      error->all(FLERR,"Label map is incomplete. "
+                 "All types must be assigned a type label.");
     atom->data_dihedrals(nchunk,buffer,count,id_offset,doffset,
                          labelflag,lmap->lmap2lmap.dihedral);
     nread += nchunk;
@@ -1603,6 +1615,9 @@ 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");
+    if (labelflag && !lmap->is_complete())
+      error->all(FLERR,"Label map is incomplete. "
+                 "All types must be assigned a type label.");
     atom->data_impropers(nchunk,buffer,count,id_offset,ioffset,
                          labelflag,lmap->lmap2lmap.improper);
     nread += nchunk;
@@ -1798,6 +1813,9 @@ void ReadData::mass()
 
   int eof = comm->read_lines_from_file(fp,ntypes,MAXLINE,buf);
   if (eof) error->all(FLERR,"Unexpected end of data file");
+  if (labelflag && !lmap->is_complete())
+    error->all(FLERR,"Label map is incomplete. "
+               "All types must be assigned a type label.");
 
   char *original = buf;
   for (int i = 0; i < ntypes; i++) {
@@ -1983,7 +2001,8 @@ void ReadData::typelabels(std::vector<std::string> &mytypelabel, int myntypes, i
   for (int i = 0; i < myntypes; i++) {
     next = strchr(buf,'\n');
     *next = '\0';
-    sscanf(buf,"%*d %s",typelabel);
+    int rv = sscanf(buf,"%*d %s",typelabel);
+    if (rv != 1) error->all(FLERR,"Invalid data file section: Type Labels");
     if (isdigit(typelabel[0])) error->all(FLERR,"Type labels cannot start with a number");
     mytypelabel[i] = typelabel;
     buf = next + 1;
@@ -2164,6 +2183,10 @@ void ReadData::skip_lines(bigint n)
 void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag,
                             int noffset, int offset, int *ilabel)
 {
+  if (labelflag && !lmap->is_complete())
+    error->all(FLERR,"Label map is incomplete. "
+               "All types must be assigned a type label.");
+
   settypeflag = 1;
   char *ptr;
   if ((ptr = strchr(line,'#'))) *ptr = '\0';