Merge pull request #3698 from yafshar/set-command-type-label

use of type labels in set commands

doc/src/set.rst

@@ -11,7 +11,16 @@ Syntax
    set style ID keyword values ...
 
 * style = *atom* or *type* or *mol* or *group* or *region*
-* ID = atom ID range or type range or mol ID range or group ID or region ID
+* ID = depends on style
+
+.. parsed-literal::
+
+       for style = *atom*, ID = a range of atom IDs
+       for style = *type*, ID = a range of numeric types or a single type label
+       for style = *mol*, ID = a range of molecule IDs
+       for style = *group*, ID = a group ID
+       for style = *region*, ID = a region ID
+
 * one or more keyword/value pairs may be appended
 * keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
   or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
@@ -28,22 +37,22 @@ Syntax
 
   .. parsed-literal::
 
-       *type* value = atom type
+       *type* value = numeric atom type or type label
          value can be an atom-style variable (see below)
        *type/fraction* values = type fraction seed
-         type = new atom type
+         type = numeric atom type or type label
          fraction = approximate fraction of selected atoms to set to new atom type
          seed = random # seed (positive integer)
        *type/ratio* values = type fraction seed
-         type = new atom type
+         type = numeric atom type or type label
          fraction = exact fraction of selected atoms to set to new atom type
          seed = random # seed (positive integer)
        *type/subset* values = type Nsubset seed
-         type = new atom type
+         type = numeric atom type or type label
          Nsubset = exact number of selected atoms to set to new atom type
          seed = random # seed (positive integer)
        *mol* value = molecule ID
-         value can be an atom-style variable (see below)
+       value can be an atom-style variable (see below)
        *x*,\ *y*,\ *z* value = atom coordinate (distance units)
          value can be an atom-style variable (see below)
        *vx*,\ *vy*,\ *vz* value = atom velocity (velocity units)
@@ -107,10 +116,10 @@ Syntax
        *image* nx ny nz
          nx,ny,nz = which periodic image of the simulation box the atom is in
          any of nx,ny,nz can be an atom-style variable (see below)
-       *bond* value = bond type for all bonds between selected atoms
+       *bond* value = numeric bond type or bond type label, for all bonds between selected atoms
-       *angle* value = angle type for all angles between selected atoms
+       *angle* value = numeric angle type or angle type label, for all angles between selected atoms
-       *dihedral* value = dihedral type for all dihedrals between selected atoms
+       *dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
-       *improper* value = improper type for all impropers between selected atoms
+       *improper* value = numeric improper type or improper type label, for all impropers between selected atoms
        *sph/e* value = energy of SPH particles (need units)
          value can be an atom-style variable (see below)
        *sph/cv* value = heat capacity of SPH particles (need units)
@@ -145,15 +154,19 @@ Examples
 .. code-block:: LAMMPS
 
    set group solvent type 2
+   set group solvent type C
    set group solvent type/fraction 2 0.5 12393
+   set group solvent type/fraction C 0.5 12393
    set group edge bond 4
    set region half charge 0.5
    set type 3 charge 0.5
+   set type H charge 0.5
    set type 1*3 charge 0.5
    set atom * charge v_atomfile
    set atom 100*200 x 0.5 y 1.0
    set atom 100 vx 0.0 vy 0.0 vz -1.0
    set atom 1492 type 3
+   set atom 1492 type H
    set atom * i_myVal 5
    set atom * d2_Sxyz[1] 6.4
 
@@ -183,9 +196,17 @@ properties to reset and what the new values are.  Some strings like
 This section describes how to select which atoms to change
 the properties of, via the *style* and *ID* arguments.
 
-The style *atom* selects all the atoms in a range of atom IDs.  The
+.. versionchanged:: 28Mar2023
-style *type* selects all the atoms in a range of types.  The style
+
-*mol* selects all the atoms in a range of molecule IDs.
+   Support for type labels was added for selecting atoms by type
+
+The style *atom* selects all the atoms in a range of atom IDs.
+
+The style *type* selects all the atoms in a range of types or type
+labels.  The style *type* selects atoms in one of two ways.  A range
+of numeric atom types can be specified.  Or a single atom type label
+can be specified, e.g. "C".  The style *mol* selects all the atoms in
+a range of molecule IDs.
 
 In each of the range cases, the range can be specified as a single
 numeric value, or a wildcard asterisk can be used to specify a range
@@ -237,14 +258,23 @@ from a file.
    such as the molecule ID, then the floating point value is truncated to
    its integer portion, e.g. a value of 2.6 would become 2.
 
-Keyword *type* sets the atom type for all selected atoms.  The
+.. versionchanged:: 28Mar2023
-specified value must be from 1 to ntypes, where ntypes was set by the
-:doc:`create_box <create_box>` command or the *atom types* field in the
-header of the data file read by the :doc:`read_data <read_data>`
-command.
 
-Keyword *type/fraction* sets the atom type for a fraction of the
+   Support for type labels was added for setting atom, bond, angle,
-selected atoms.  The actual number of atoms changed is not guaranteed
+   dihedral, and improper types
+
+Keyword *type* sets the atom type for all selected atoms.  A specified
+value can be either a numeric atom type or an atom type label. When
+using a numeric type, the specified value must be from 1 to ntypes,
+where ntypes was set by the :doc:`create_box <create_box>` command or
+the *atom types* field in the header of the data file read by the
+:doc:`read_data <read_data>` command.  When using a type label it must
+have been defined previously.  See the :doc:`Howto type labels
+<Howto_type_labels>` doc page for the allowed syntax of type labels
+and a general discussion of how type labels can be used.
+
+Keyword *type/fraction* sets the atom type for a fraction of the selected
+atoms.  The actual number of atoms changed is not guaranteed
 to be exactly the specified fraction (0 <= *fraction* <= 1), but
 should be statistically close.  Random numbers are used in such a way
 that a particular atom is changed or not changed, regardless of how
@@ -463,14 +493,18 @@ simulation, but may mess up analysis of the trajectories if a LAMMPS
 diagnostic or your own analysis relies on the image flags to unwrap a
 molecule which straddles the periodic box.
 
-Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond type
+Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
-(angle type, etc) of all bonds (angles, etc) of selected atoms to the
+type (angle type, etc) of all bonds (angles, etc) of selected atoms to
-specified value from 1 to nbondtypes (nangletypes, etc).  All atoms in a
+the specified value.  The value can be a numeric type from 1 to
-particular bond (angle, etc) must be selected atoms in order for the
+nbondtypes (nangletypes, etc).  Or it can be a type label (bond type
-change to be made.  The value of nbondtype (nangletypes, etc) was set by
+label, angle type lable, etc).  See the :doc:`Howto type labels
-the *bond types* (\ *angle types*, etc) field in the header of the data
+<Howto_type_labels>` doc page for the allowed syntax of type labels
-file read by the :doc:`read_data <read_data>` command.  These keywords
+and a general discussion of how type labels can be used.  All atoms in
-do not allow use of an atom-style variable.
+a particular bond (angle, etc) must be selected atoms in order for the
+change to be made.  The value of nbondtypes (nangletypes, etc) was set
+by the *bond types* (\ *angle types*, etc) field in the header of the
+data file read by the :doc:`read_data <read_data>` command.  These
+keywords do not allow use of an atom-style variable.
 
 Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
 and density of smoothed particle hydrodynamics (SPH) particles.  See

src/atom.cpp

@@ -1944,16 +1944,17 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
     error->all(file,line, "Cannot set per-type atom mass for atom style {}", atom_style);
 
   char *typestr = utils::expand_type(file, line, arg[0], Atom::ATOM, lmp);
-  if (typestr) arg[0] = typestr;
+  const std::string str = typestr ? typestr : arg[0];
+  delete[] typestr;
 
   int lo, hi;
-  utils::bounds(file, line, arg[0], 1, ntypes, lo, hi, error);
+  utils::bounds(file, line, str, 1, ntypes, lo, hi, error);
   if ((lo < 1) || (hi > ntypes))
-    error->all(file, line, "Invalid atom type {} for atom mass", arg[0]);
+    error->all(file, line, "Invalid atom type {} for atom mass", str);
 
   const double value = utils::numeric(FLERR, arg[1], false, lmp);
   if (value <= 0.0)
-    error->all(file, line, "Invalid atom mass value {} for type {}", value, arg[0]);
+    error->all(file, line, "Invalid atom mass value {} for type {}", value, str);
 
   for (int itype = lo; itype <= hi; itype++) {
     mass[itype] = value;

src/set.cpp

@@ -93,13 +93,19 @@ void Set::command(int narg, char **arg)
     if (strcmp(arg[iarg],"type") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set type", error);
       if (utils::strmatch(arg[iarg+1],"^v_")) varparse(arg[iarg+1],1);
-      else ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      else {
+        char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp);
+        ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+        delete[] typestr;
+      }
       set(TYPE);
       iarg += 2;
 
     } else if (strcmp(arg[iarg],"type/fraction") == 0) {
       if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/fraction", error);
-      newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp);
+      newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp);
       ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
       if (newtype <= 0 || newtype > atom->ntypes)
@@ -113,7 +119,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"type/ratio") == 0) {
       if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/ratio", error);
-      newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp);
+      newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp);
       ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
       if (newtype <= 0 || newtype > atom->ntypes)
@@ -127,7 +135,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"type/subset") == 0) {
       if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "set type/subset", error);
-      newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ATOM,lmp);
+      newtype = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       nsubset = utils::bnumeric(FLERR,arg[iarg+2],false,lmp);
       ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
       if (newtype <= 0 || newtype > atom->ntypes)
@@ -477,7 +487,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"bond") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set bond", error);
-      ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::BOND,lmp);
+      ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       if (atom->avec->bonds_allow == 0)
         error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
       if (ivalue <= 0 || ivalue > atom->nbondtypes)
@@ -487,7 +499,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"angle") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set angle", error);
-      ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::ANGLE,lmp);
+      ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       if (atom->avec->angles_allow == 0)
         error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
       if (ivalue <= 0 || ivalue > atom->nangletypes)
@@ -497,7 +511,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"dihedral") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set dihedral", error);
-      ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::DIHEDRAL,lmp);
+      ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       if (atom->avec->dihedrals_allow == 0)
         error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
       if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
@@ -507,7 +523,9 @@ void Set::command(int narg, char **arg)
 
     } else if (strcmp(arg[iarg],"improper") == 0) {
       if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "set improper", error);
-      ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
+      char *typestr = utils::expand_type(FLERR,arg[iarg+1],Atom::IMPROPER,lmp);
+      ivalue = utils::inumeric(FLERR,typestr?typestr:arg[iarg+1],false,lmp);
+      delete[] typestr;
       if (atom->avec->impropers_allow == 0)
         error->all(FLERR,"Cannot set attribute {} for atom style {}", arg[iarg], atom->get_style());
       if (ivalue <= 0 || ivalue > atom->nimpropertypes)
@@ -742,6 +760,10 @@ void Set::selection(int n)
       else select[i] = 0;
 
   } else if (style == TYPE_SELECT) {
+    if (char *typestr = utils::expand_type(FLERR,id,Atom::ATOM,lmp)) {
+      delete[] id;
+      id = typestr;
+    }
     utils::bounds(FLERR,id,1,atom->ntypes,nlo,nhi,error);
 
     int *type = atom->type;

unittest/commands/test_set_property.cpp

@@ -206,6 +206,16 @@ TEST_F(SetTest, StylesTypes)
         sum += (atom->type[i] == 2) ? 1 : 0;
     ASSERT_EQ(sum, 4);
 
+    BEGIN_HIDE_OUTPUT();
+    command("labelmap atom 1 C 2 H");
+    command("set group all type C");
+    command("set group all type/fraction H 0.5 453246");
+    END_HIDE_OUTPUT();
+    sum = 0;
+    for (int i = 0; i < 8; ++i)
+        sum += (atom->type[i] == 2) ? 1 : 0;
+    ASSERT_EQ(sum, 4);
+
     BEGIN_HIDE_OUTPUT();
     command("set group all type 1");
     command("set group all type/ratio 2 0.5 5784536");
@@ -224,6 +234,15 @@ TEST_F(SetTest, StylesTypes)
         sum += (atom->type[i] == 2) ? 1 : 0;
     ASSERT_EQ(sum, 4);
 
+    BEGIN_HIDE_OUTPUT();
+    command("set group all type C");
+    command("set group all type/subset H 5 784536");
+    END_HIDE_OUTPUT();
+    sum = 0;
+    for (int i = 0; i < 8; ++i)
+        sum += (atom->type[i] == 2) ? 1 : 0;
+    ASSERT_EQ(sum, 5);
+
     TEST_FAILURE(".*ERROR: Numeric index 9 is out of bounds .1-8.*", command("set type 9 x 0.0"););
     TEST_FAILURE(".*ERROR: Invalid range string: 3:10.*", command("set type 3:10 x 0.0"););
     TEST_FAILURE(".*ERROR: Could not find set group ID nope.*", command("set group nope x 0.0"););
@@ -247,6 +266,34 @@ TEST_F(SetTest, PosVelCharge)
     ASSERT_EQ(atom->q[6], -1);
     ASSERT_EQ(atom->q[7], -1);
 
+    BEGIN_HIDE_OUTPUT();
+    command("labelmap atom 1 C 2 H");
+    command("set region right type H");
+    END_HIDE_OUTPUT();
+
+    ASSERT_EQ(atom->type[0], 1);
+    ASSERT_EQ(atom->type[1], 2);
+    ASSERT_EQ(atom->type[2], 1);
+    ASSERT_EQ(atom->type[3], 2);
+    ASSERT_EQ(atom->type[4], 1);
+    ASSERT_EQ(atom->type[5], 2);
+    ASSERT_EQ(atom->type[6], 1);
+    ASSERT_EQ(atom->type[7], 2);
+
+    BEGIN_HIDE_OUTPUT();
+    command("set type C charge 1.25");
+    command("set type H charge -1.25");
+    END_HIDE_OUTPUT();
+
+    ASSERT_EQ(atom->q[0], 1.25);
+    ASSERT_EQ(atom->q[1], -1.25);
+    ASSERT_EQ(atom->q[2], 1.25);
+    ASSERT_EQ(atom->q[3], -1.25);
+    ASSERT_EQ(atom->q[4], 1.25);
+    ASSERT_EQ(atom->q[5], -1.25);
+    ASSERT_EQ(atom->q[6], 1.25);
+    ASSERT_EQ(atom->q[7], -1.25);
+
     BEGIN_HIDE_OUTPUT();
     command("variable xpos atom 0.5-x");
     command("variable ypos atom y*0.5");