read_data: bond, etc. direct label support

doc/src/read_data.rst

@@ -587,7 +587,7 @@ label maps.
   .. parsed-literal::
 
        ID = number of angle (1-Nangles)
-       type = angle type (1-Nangletype)
+       type = angle type (1-Nangletype, or type label)
        atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
 
 example:
@@ -631,23 +631,24 @@ atom, bond, etc. types in terms of user-provided strings instead of
 numbers.  If a type label section exists for a given interaction
 (atom, bond, angle, dihedral or improper), then all types must be
 assigned a type label for that interaction.  Type label sections must
-come before any section that utilizes that type.  The numeric types
+come before any section that utilizes that type.  Type labels can be
-listed in the *Atoms*, *Bonds*, etc. section are first converted into
+directly substituted for numeric types listed in the *Atoms*, *Bonds*,
-their corresponding type label before being read into LAMMPS; type
+etc. sections of data files. If numeric types are used, each
-labels cannot be directly substituted for numeric types used in data
+interaction type is first converted into its corresponding type label
-files.  Data files assign all types to the default label map; if the
+before being read into LAMMPS.  Data files assign all types to the
-type label does not already exist, the type label is created as a new
+default label map; if the type label does not already exist, the type
-type and assigned to the default label map.  The corresponding
+label is created as a new type and assigned to the default label map.
-interaction coefficients listed in the data file are associated to
+The corresponding interaction coefficients listed in the data file are
-this type.  There must be enough space in the per-type data
+associated to this type.  There must be enough space in the per-type
-arrays to create new types; see the *extra/atom/types* keyword for how
+data arrays to create new types; see the *extra/atom/types* keyword
-to reserve extra space for new types, e.g., when reading multiple data
+for how to reserve extra space for new types, e.g., when reading
-files.  Note that, in this case, the numeric-to-label mapping within a
+multiple data files.  Note that, in this case, the numeric-to-label
-data file does not necessary correspond to that of the simulation;
+mapping within a data file does not necessary correspond to that of
-once the default label map is fully defined, the :doc:`write_data <write_data>`
+the simulation; once the default label map is fully defined, the
-command can be used to print out the default label map at a given
+:doc:`write_data <write_data>` command can be used to print out the
-point in a simulation.  See the :doc:`labelmap <labelmap>` command for
+default label map at a given point in a simulation.  See the
-more discussion on how to use type label maps.
+:doc:`labelmap <labelmap>` command for more discussion on how to use
+type label maps.
 
 ----------
 
@@ -720,7 +721,7 @@ of analysis.
 The per-atom values have these meanings and units, listed alphabetically:
 
 * atom-ID = integer ID of atom
-* atom-type = type of atom (1-Ntype)
+* atom-type = type of atom (1-Ntype, or type label)
 * bodyflag = 1 for body particles, 0 for point particles
 * bond_nt = bond NT factor for MESONT particles (?? units)
 * buckling = buckling factor for MESONT particles (?? units)
@@ -1044,7 +1045,7 @@ label maps.
   .. parsed-literal::
 
        ID = bond number (1-Nbonds)
-       type = bond type (1-Nbondtype)
+       type = bond type (1-Nbondtype, or type label)
        atom1,atom2 = IDs of 1st,2nd atom in bond
 
 * example:
@@ -1108,7 +1109,7 @@ use type label maps.
   .. parsed-literal::
 
        ID = number of dihedral (1-Ndihedrals)
-       type = dihedral type (1-Ndihedraltype)
+       type = dihedral type (1-Ndihedraltype, or type label)
        atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
 
 * example:
@@ -1227,7 +1228,7 @@ use type label maps.
   .. parsed-literal::
 
        ID = number of improper (1-Nimpropers)
-       type = improper type (1-Nimpropertype)
+       type = improper type (1-Nimpropertype, or type label)
        atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
 
 * example:

doc/src/write_data.rst

@@ -118,7 +118,8 @@ etc. types are written in the Atoms, Bonds, etc. sections. If the
 value is specified as *numeric*, then numeric types are used. If the
 value is specified as *labels*, then interaction types are written as
 type labels using the default label map. When using type labels, the
-default label map must be written to the data file.
+default label map (i.e., Type Label sections) must be 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/atom.cpp

@@ -53,6 +53,7 @@ using namespace MathConst;
 #define DELTA 1
 #define DELTA_PERATOM 64
 #define EPSILON 1.0e-6
+#define MAXLINE 256
 
 /* ---------------------------------------------------------------------- */
 
@@ -1198,9 +1199,9 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
       if (id_offset) tag[nlocal-1] += id_offset;
       if (mol_offset) molecule[nlocal-1] += mol_offset;
       if (!isdigit(typestr[0])) {
-        if (!atom->labelmapflag) error->one(FLERR,"Invalid Types section in molecule file");
+        if (!atom->labelmapflag) error->one(FLERR,"Invalid Atoms section in data file");
         type[nlocal-1] = atom->find_label(typestr,Atom::ATOM);
-        if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Types section in molecule file");
+        if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Atoms section in data file");
       } else {
         type[nlocal-1] = utils::inumeric(FLERR,typestr.c_str(),true,lmp);
         if (labelflag) type[nlocal-1] = ilabel[type[nlocal-1]-1];
@@ -1275,20 +1276,30 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
   int m,tmp,itype,rv;
   tagint atom1,atom2;
   char *next;
+  char typechar[MAXLINE];
+  std::string typestr;
   int newton_bond = force->newton_bond;
 
   for (int i = 0; i < n; i++) {
     next = strchr(buf,'\n');
     *next = '\0';
-    rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
+    rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT,
-                &tmp,&itype,&atom1,&atom2);
+                &tmp,typechar,&atom1,&atom2);
     if (rv != 4)
       error->one(FLERR,"Incorrect format of Bonds section in data file");
     if (id_offset) {
       atom1 += id_offset;
       atom2 += id_offset;
     }
+    typestr = typechar;
+    if (!isdigit(typestr[0])) {
+      if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in data file");
+      itype = atom->find_label(typestr,Atom::BOND);
+      if (itype == -1) error->one(FLERR,"Invalid Bonds section in data file");
+    } else {
+      itype = utils::inumeric(FLERR,typechar,true,lmp);
       if (labelflag) itype = ilabel[itype-1];
+    }
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1333,13 +1344,15 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3;
   char *next;
+  char typechar[MAXLINE];
+  std::string typestr;
   int newton_bond = force->newton_bond;
 
   for (int i = 0; i < n; i++) {
     next = strchr(buf,'\n');
     *next = '\0';
-    rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+    rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
-                &tmp,&itype,&atom1,&atom2,&atom3);
+                &tmp,typechar,&atom1,&atom2,&atom3);
     if (rv != 5)
       error->one(FLERR,"Incorrect format of Angles section in data file");
     if (id_offset) {
@@ -1347,7 +1360,15 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
       atom2 += id_offset;
       atom3 += id_offset;
     }
+    typestr = typechar;
+    if (!isdigit(typestr[0])) {
+      if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in data file");
+      itype = atom->find_label(typestr,Atom::ANGLE);
+      if (itype == -1) error->one(FLERR,"Invalid Angles section in data file");
+    } else {
+      itype = utils::inumeric(FLERR,typechar,true,lmp);
       if (labelflag) itype = ilabel[itype-1];
+    }
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1406,14 +1427,16 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3,atom4;
   char *next;
+  char typechar[MAXLINE];
+  std::string typestr;
   int newton_bond = force->newton_bond;
 
   for (int i = 0; i < n; i++) {
     next = strchr(buf,'\n');
     *next = '\0';
-    rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
+    rv = sscanf(buf,"%d %s " TAGINT_FORMAT " " TAGINT_FORMAT
                 " " TAGINT_FORMAT " " TAGINT_FORMAT,
-                &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+                &tmp,typechar,&atom1,&atom2,&atom3,&atom4);
     if (rv != 6)
       error->one(FLERR,"Incorrect format of Dihedrals section in data file");
     if (id_offset) {
@@ -1422,7 +1445,15 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
       atom3 += id_offset;
       atom4 += id_offset;
     }
+    typestr = typechar;
+    if (!isdigit(typestr[0])) {
+      if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in data file");
+      itype = atom->find_label(typestr,Atom::DIHEDRAL);
+      if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in data file");
+    } else {
+      itype = utils::inumeric(FLERR,typechar,true,lmp);
       if (labelflag) itype = ilabel[itype-1];
+    }
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||
@@ -1498,14 +1529,16 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
   int m,tmp,itype,rv;
   tagint atom1,atom2,atom3,atom4;
   char *next;
+  char typechar[MAXLINE];
+  std::string typestr;
   int newton_bond = force->newton_bond;
 
   for (int i = 0; i < n; i++) {
     next = strchr(buf,'\n');
     *next = '\0';
-    rv = sscanf(buf,"%d %d "
+    rv = sscanf(buf,"%d %s "
                 TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
-                &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+                &tmp,typechar,&atom1,&atom2,&atom3,&atom4);
     if (rv != 6)
       error->one(FLERR,"Incorrect format of Impropers section in data file");
     if (id_offset) {
@@ -1514,7 +1547,15 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
       atom3 += id_offset;
       atom4 += id_offset;
     }
+    typestr = typechar;
+    if (!isdigit(typestr[0])) {
+      if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in data file");
+      itype = atom->find_label(typestr,Atom::IMPROPER);
+      if (itype == -1) error->one(FLERR,"Invalid Impropers section in data file");
+    } else {
+      itype = utils::inumeric(FLERR,typechar,true,lmp);
       if (labelflag) itype = ilabel[itype-1];
+    }
     itype += type_offset;
 
     if ((atom1 <= 0) || (atom1 > map_tag_max) ||