revise/refacor Type Label section parsing and Atoms section parsing

- do not ignore numeric type in Type Label sections
- refuse invalid numeric types that will overflow arrays
- check for duplicate numeric type entries or non-unique labels
- better error messages
- use Tokenizer class instead of sscanf()

doc/src/labelmap.rst

@@ -24,8 +24,8 @@ Examples
 
 .. code-block:: LAMMPS
 
-   labelmap atom 3 carbon
+   labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
-   labelmap bond 1 carbonyl 2 nitrile
+   labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
    labelmap atom $(label(carbon)) C  # change type label from 'carbon' to 'C'
    labelmap clear
    labelmap write mymap.include
@@ -46,29 +46,33 @@ Bond Type Labels, etc.  See the :doc:`Howto type labels
 labels can be used.
 
 Valid type labels may contain any alphanumeric character, but must not
-start with a number.  They can also contain other standard ASCII
+start with a number, a '#', or a '*' character.  They may contain other
-characters such as angular or square brackets '<' and '>' or '[' and
+standard ASCII characters such as angular or square brackets '<' and '>'
-']', parenthesis '(' and ')', dash '-', underscore '_', plus '+' and
+or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
-equals '=' signs and more.  Note that type labels must be put in
+'+' and equals '=' signs and more.  The must not contain blanks or any
-quotation marks if they contain the '#' character when used in a context
+other whitespace.  Note that type labels must be put in single or double
-where the '#' character would be interpreted as starting a comment like
+quotation marks if they contain the '#' character, or a double (") or
-in the LAMMPS input file.
+single quotation mark ("). If the label contains both, single and double
+quotes, triple quotation (""") must be used.  When using quotation
+marks, the LAMMPS input parser may require adding leading or trailing
+blanks so it can identify the quotation marks. Those blanks will be
+removed when defining the label.
 
 A *labelmap* command can only modify the label map for one type-kind
 (atom types, bond types, etc).  Any number of numeric-type/type-label
-pairs may follow.  If a type label already exists for a given numeric
+pairs may follow.  If a type label already exists for the same numeric
-type, it will be overwritten.  Type labels must be unique; assigning
+type, it will be overwritten.  Type labels must be unique; assigning the
-the same type label to multiple numeric types is not allowed.  In some
+same type label to multiple numeric types is not allowed.  In some
-cases, such as when reading and writing data files, it is required
+cases, such as when reading and writing data files, it is required that
-that when type labels are used, that there is a label defined for
+when type labels are used, that there is a label defined for *every*
-*every* numeric type.
+numeric type.
 
 The *clear* option resets the labelmap and thus discards all previous
 settings.
 
 The *write* option takes a filename as argument and writes the current
 label mappings to a file as labelmap commands, so the file can be copied
-into a different LAMMPS input file or read using the :doc:`include
+into a new LAMMPS input file or read in using the :doc:`include
 <include>` command.
 
 ----------

src/atom.cpp

@@ -87,7 +87,7 @@ are updated by the AtomVec class as needed.
  * instances of classes derived from the AtomVec base
  * class, which correspond to the selected atom style.
  *
- * \param  lmp  pointer to the base LAMMPS class */
+ * \param  _lmp  pointer to the base LAMMPS class */
 
 Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
 {
@@ -1186,17 +1186,36 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
         avec->data_atom(xdata,imagedata,values,typestr);
         if (id_offset) tag[nlocal-1] += id_offset;
         if (mol_offset) molecule[nlocal-1] += mol_offset;
-        if (!isdigit(typestr[0])) {
+        // clang-format on
-          if (!atom->labelmapflag) error->one(FLERR,"Invalid Atoms section in data file");
+        switch (utils::is_type(typestr)) {
-          type[nlocal-1] = lmap->find(typestr,Atom::ATOM);
+
-          if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Atoms section in data file");
+          case 0: {    // numeric
-        } else {
+            int itype = utils::inumeric(FLERR, typestr.c_str(), true, lmp);
-          type[nlocal-1] = utils::inumeric(FLERR,typestr.c_str(),true,lmp);
+            if ((itype < 1) || (itype > ntypes))
-          if (labelflag) type[nlocal-1] = ilabel[type[nlocal-1]-1];
+              error->one(FLERR, "Invalid atom type {} in Atoms section of data file: {}", itype,
+                         buf);
+            type[nlocal - 1] = itype;
+            if (labelflag) type[nlocal - 1] = ilabel[itype - 1];
+            break;
+          }
+
+          case 1: {    // type label
+            if (!atom->labelmapflag)
+              error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
+            type[nlocal - 1] = lmap->find(typestr, Atom::ATOM);
+            if (type[nlocal - 1] == -1)
+              error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
+            break;
+          }
+
+          default:    // invalid
+            error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
+            break;
         }
+        // clang-format off
         if (type_offset) type[nlocal-1] += type_offset;
         if (type[nlocal-1] <= 0 || type[nlocal-1] > ntypes)
-          error->one(FLERR,"Invalid atom type in Atoms section of data file");
+          error->one(FLERR,"Invalid atom type {} in Atoms section of data file", typestr);
       }
     }
     buf = next + 1;

src/read_data.cpp

@@ -82,6 +82,8 @@ enum{NONE, APPEND, VALUE, MERGE};
 static const char *suffixes[] = {"/cuda", "/gpu", "/opt", "/omp", "/kk", "/coul/cut", "/coul/long",
                                  "/coul/msm", "/coul/dsf", "/coul/debye", "/coul/charmm", nullptr};
 
+static const char *labeltypes[] = {"Atom", "Bond", "Angle", "Dihedral", "Improper" };
+
 // clang-format on
 /* ---------------------------------------------------------------------- */
 ReadData::ReadData(LAMMPS *_lmp) : Command(_lmp), fp(nullptr), coeffarg(nullptr), lmap(nullptr)
@@ -1322,9 +1324,7 @@ void ReadData::atoms()
     eof = utils::read_lines_from_file(fp, nchunk, MAXLINE, buffer, me, world);
     if (eof) error->all(FLERR, "Unexpected end of data file");
     if (tlabelflag && !lmap->is_complete(Atom::ATOM))
-      error->all(FLERR,
+      error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
-                 "Label map is incomplete: "
-                 "all types must be assigned a unique type label");
     atom->data_atoms(nchunk, buffer, id_offset, mol_offset, toffset, shiftflag, shift, tlabelflag,
                      lmap->lmap2lmap.atom);
     nread += nchunk;
@@ -2144,21 +2144,38 @@ void ReadData::typelabels(int mode)
   int eof = utils::read_lines_from_file(fp, lntypes, MAXLINE, buf, me, world);
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
-  char *next;
   char *original = buf;
-  char *typelabel = new char[MAXLINE];
+  char *next;
   for (int i = 0; i < lntypes; i++) {
     next = strchr(buf, '\n');
     *next = '\0';
-    int rv = sscanf(buf, "%*d %s", typelabel);
+    auto values = Tokenizer(buf).as_vector();
-    if (rv != 1) error->all(FLERR, "Invalid data file section: Type Labels");
+    int nwords = values.size();
-    if (isdigit(typelabel[0])) error->all(FLERR, "Type labels cannot start with a number");
+    for (std::size_t ii = 0; ii < values.size(); ++ii) {
-    (*labels)[i] = typelabel;
+      if (utils::strmatch(values[ii],"^#")) {
-    (*labels_map)[typelabel] = i + 1;
+        nwords = ii;
+        break;
+      }
+    }
+    if (nwords != 2)
+      error->all(FLERR, "Invalid format in section: {} Type Labels: {}", labeltypes[mode], buf);
+    if (utils::is_type(values[1]) != 1) error->all(FLERR, "Invalid type label {}", values[1]);
+    int itype = utils::inumeric(FLERR, values[0], false, lmp);
+    if ((itype < 1) || (itype > lntypes))
+      error->all(FLERR, "Invalid type {} in section: {} Type Labels: {}", labeltypes[mode], buf);
+    
+    (*labels)[itype - 1] = values[1];
+    (*labels_map)[values[1]] = itype;
     buf = next + 1;
   }
   delete[] original;
-  delete[] typelabel;
+
+  for (int i = 0; i < lntypes; ++i) {
+    if ((*labels)[i].empty())
+      error->all(FLERR, "{} Type Labels map is incomplete", labeltypes[mode]);
+  }
+  if ((int)(*labels_map).size() != lntypes)
+    error->all(FLERR, "{} Type Labels map is incomplete", labeltypes[mode]);
 
   // merge this read_data label map to atom class
   // determine mapping to let labels override numeric types

unittest/commands/test_labelmap.cpp

@@ -49,42 +49,6 @@ protected:
     }
 
     void TearDown() override { LAMMPSTest::TearDown(); }
-
-    void atomic_system(const std::string &atom_style, const std::string units = "real")
-    {
-        BEGIN_HIDE_OUTPUT();
-        command("atom_style " + atom_style);
-        command("atom_modify map array");
-        command("units " + units);
-        command("lattice sc 1.0 origin 0.125 0.125 0.125");
-        command("region box block 0 2 0 2 0 2");
-        command("create_box 8 box");
-        command("create_atoms 1 box");
-        command("mass * 1.0");
-        command("region left block 0.0 1.0 INF INF INF INF");
-        command("region right block 1.0 2.0 INF INF INF INF");
-        command("region top block INF INF 0.0 1.0 INF INF");
-        command("region bottom block INF INF 1.0 2.0 INF INF");
-        command("region front block INF INF INF INF 0.0 1.0");
-        command("region back block INF INF INF 1.0 2.0 INF");
-        command("group top region top");
-        command("group bottom region bottom");
-        END_HIDE_OUTPUT();
-    }
-
-    bool molecular_system()
-    {
-        if (info->has_style("atom", "full")) {
-            BEGIN_HIDE_OUTPUT();
-            command("variable input_dir index \"" STRINGIFY(TEST_INPUT_FOLDER) "\"");
-            command("include \"${input_dir}/in.fourmol\"");
-            command("group allwater molecule 3:6");
-            command("region half block 0.0 INF INF INF INF INF");
-            END_HIDE_OUTPUT();
-            return true;
-        } else
-            return false;
-    }
 };
 
 TEST_F(SetTest, NoBoxAtoms)

unittest/commands/test_set_property.cpp

@@ -316,7 +316,7 @@ TEST_F(SetTest, SpinPackage)
     constexpr double vx   = 0.1;
     constexpr double vy   = 0.5;
     constexpr double vz   = -0.1;
-    constexpr double norm = 1.0 / sqrt(vx * vx + vy * vy + vz * vz);
+    const double norm = 1.0 / sqrt(vx * vx + vy * vy + vz * vz);
     ASSERT_EQ(atom->sp[0][0], vx * norm);
     ASSERT_EQ(atom->sp[0][1], vy * norm);
     ASSERT_EQ(atom->sp[0][2], vz * norm);