add "labelmap clear" command, update docs

doc/src/labelmap.rst

@@ -8,11 +8,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   labelmap type-kind numeric-type type-label ... keyword arg
+   labelmap option args
 
-* type-kind = *atom* or *bond* or *angle* or *dihedral* or *improper*
+* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear*
-* one or more numeric-type/type-label pairs may be specified
+* except for the *clear* option, one or more numeric-type/type-label pairs may be appended
-* zero or more keyword/arg pairs may be appended
 
 Examples
 """"""""
@@ -22,6 +21,7 @@ Examples
    labelmap atom 3 carbon
    labelmap bond 1 carbonyl 2 nitrile
    labelmap atom $(label(carbon)) C  # change type label from 'carbon' to 'C'
+   labelmap clear
 
 Description
 """""""""""
@@ -40,7 +40,7 @@ As explained on the Howto page, valid type labels can contain any
 alphanumeric character, but cannot start with a number.  They can also
 contain standard characters such as square brackets "[" and "]", dash
 "-", underscore "_", plus "+" and equals "=" signs.  Note that type
-labels cannot contain the comment symbol '#'.
+labels must be put in quotation marks if they contain the comment symbol '#'.
 
 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
@@ -51,6 +51,9 @@ cases, such as when reading and writing data files, it is required
 that a type label be defined for every numeric type (within a given
 type-kind).
 
+The *clear* option resets the labelmap and thus discards all previous
+settings.
+
 ----------
 
 Restrictions

src/label_map.cpp

@@ -33,7 +33,7 @@ LabelMap::LabelMap(LAMMPS *_lmp, int _natomtypes, int _nbondtypes, int _nanglety
 {
   lmap2lmap.atom = lmap2lmap.bond = lmap2lmap.angle = lmap2lmap.dihedral = lmap2lmap.improper =
       nullptr;
-  allocate_type_labels();
+  reset_type_labels();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -48,40 +48,45 @@ LabelMap::~LabelMap()
 }
 
 /* ----------------------------------------------------------------------
-   allocate character-based type arrays (labels) of length ntypes
+   reset/allocate character-based type arrays (labels) of length ntypes
 ------------------------------------------------------------------------- */
 
-void LabelMap::allocate_type_labels()
+void LabelMap::reset_type_labels()
 {
+  typelabel_map.clear();
   typelabel.resize(natomtypes);
   delete[] lmap2lmap.atom;
   lmap2lmap.atom = new int[natomtypes];
   for (auto &i : typelabel) i.clear();
   memset(lmap2lmap.atom, 0, natomtypes * sizeof(int));
 
+  btypelabel_map.clear();
   btypelabel.resize(nbondtypes);
   delete[] lmap2lmap.bond;
   for (auto &i : btypelabel) i.clear();
   lmap2lmap.bond = new int[nbondtypes];
   memset(lmap2lmap.bond, 0, nbondtypes * sizeof(int));
 
+  atypelabel_map.clear();
   atypelabel.resize(nangletypes);
   delete[] lmap2lmap.angle;
   for (auto &i : atypelabel) i.clear();
   lmap2lmap.angle = new int[nangletypes];
   memset(lmap2lmap.angle, 0, nangletypes * sizeof(int));
 
+  dtypelabel_map.clear();
   dtypelabel.resize(ndihedraltypes);
   delete[] lmap2lmap.dihedral;
   for (auto &i : dtypelabel) i.clear();
   lmap2lmap.dihedral = new int[ndihedraltypes];
   memset(lmap2lmap.dihedral, 0, ndihedraltypes * sizeof(int));
 
+  itypelabel_map.clear();
   itypelabel.resize(nimpropertypes);
   delete[] lmap2lmap.improper;
   for (auto &i : itypelabel) i.clear();
   lmap2lmap.improper = new int[nimpropertypes];
-  memset(lmap2lmap.dihedral, 0, nimpropertypes * sizeof(int));
+  memset(lmap2lmap.improper, 0, nimpropertypes * sizeof(int));
 }
 
 /* ----------------------------------------------------------------------
@@ -90,7 +95,7 @@ void LabelMap::allocate_type_labels()
 
 void LabelMap::modify_lmap(int narg, char **arg)
 {
-  if (narg < 3 || narg % 2 == 0)
+  if ((narg < 1) || ((narg > 2) && ((narg % 2) == 0)))
     error->all(FLERR, "Incorrect number of arguments for labelmap command");
 
   int ntypes;
@@ -117,11 +122,17 @@ void LabelMap::modify_lmap(int narg, char **arg)
     ntypes = nimpropertypes;
     labels = &itypelabel;
     labels_map = &itypelabel_map;
+  } else if (tlabel == "clear") {
+    if (narg != 1) error->all(FLERR, "Incorrect number of arguments for labelmap command");
+    reset_type_labels();
+    return;
   } else
-    error->all(FLERR, "Unknown labelmap type {}", tlabel);
+    error->all(FLERR, "Unknown labelmap keyword {}", tlabel);
 
   int iarg = 1;
+  if (narg == 1) utils::missing_cmd_args(FLERR, "labelmap " + tlabel, error);
   while (iarg < narg) {
+    if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "labelmap " + tlabel, error);
     if (ntypes < 1) error->all(FLERR, "No {} types allowed with current box settings", tlabel);
     int itype = utils::inumeric(FLERR, arg[iarg++], false, lmp);
     if ((itype < 1) || (itype > ntypes))
@@ -130,7 +141,8 @@ void LabelMap::modify_lmap(int narg, char **arg)
     if (isdigit(slabel[0]))
       error->all(FLERR, "Label {} for {} type {} must not start with a number", slabel, tlabel,
                  itype);
-    if (search(slabel, (*labels_map)) != -1)
+    int found = search(slabel, (*labels_map));
+    if ((found != -1) && (found != itype))
       error->all(FLERR, "The {} type label {} is already in use for type {}", tlabel, slabel,
                  (*labels_map)[slabel]);
     std::string &str = (*labels)[itype - 1];

src/label_map.h

@@ -61,7 +61,7 @@ class LabelMap : protected Pointers {
 
   Lmap2Lmap lmap2lmap;
 
-  void allocate_type_labels();
+  void reset_type_labels();
   int find_or_create(const std::string &, std::vector<std::string> &,
                      std::unordered_map<std::string, int> &);    // look up type or create new type
   int search(const std::string &,

unittest/commands/test_labelmap.cpp

@@ -105,13 +105,13 @@ TEST_F(SetTest, NoBoxAtoms)
     ASSERT_FALSE(atom->lmap->is_complete(Atom::ATOM));
 
     BEGIN_HIDE_OUTPUT();
-    command("labelmap atom 1 C1 2 N2");
+    command("labelmap atom 1 C1 2 N2 3 'O#' 1 C1 4 H#");
     END_HIDE_OUTPUT();
     ASSERT_TRUE(atom->lmap->is_complete(Atom::ATOM));
     ASSERT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
     ASSERT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
-    ASSERT_EQ(atom->lmap->find("O1", Atom::ATOM), 3);
+    ASSERT_EQ(atom->lmap->find("O#", Atom::ATOM), 3);
-    ASSERT_EQ(atom->lmap->find("H1", Atom::ATOM), 4);
+    ASSERT_EQ(atom->lmap->find("H", Atom::ATOM), 4);
 
     TEST_FAILURE(".*ERROR: Labelmap atom type 0 must be within 1-4.*",
                  command("labelmap atom 0 C1"););
@@ -136,9 +136,19 @@ TEST_F(SetTest, NoBoxAtoms)
     TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap command.*",
                  command("labelmap atom 1 C1 atom 2 C2"););
     TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap command.*",
+                 command("labelmap clear atom"););
+    TEST_FAILURE(".*ERROR: Illegal labelmap atom command: missing argument.*",
                  command("labelmap atom 1"););
-    TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap command.*",
+    TEST_FAILURE(".*ERROR: Illegal labelmap atom command: missing argument.*",
                  command("labelmap atom"););
+
+    BEGIN_HIDE_OUTPUT();
+    command("labelmap clear");
+    command("labelmap atom 3 C1 2 N2");
+    END_HIDE_OUTPUT();
+    ASSERT_FALSE(atom->lmap->is_complete(Atom::ATOM));
+    ASSERT_EQ(atom->lmap->find("C1", Atom::ATOM), 3);
+    ASSERT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
 }
 
 } // namespace LAMMPS_NS