groups in molecule templates: docs

doc/src/Errors_messages.rst

@@ -4732,7 +4732,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Invalid molecule ID in molecule file*
    Molecule ID must be a non-zero positive integer.
 
-*Invalid Molecules section in molecule file*   
+*Invalid Molecules section in molecule file*
    Self-explanatory.
 
 *Invalid REAX atom type*
@@ -4801,6 +4801,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Atom IDs must be positive integers and within range of defined
    atoms.
 
+*Invalid atom ID in Groups section of molecule file*
+   Self-explanatory.
+
 *Invalid atom ID in Impropers section of data file*
    Atom IDs must be positive integers and within range of defined
    atoms.

doc/src/molecule.rst

@@ -148,6 +148,7 @@ appear if the value(s) are different than the default.
 * Na *angles* = # of angles Na in molecule, default = 0
 * Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
 * Ni *impropers* = # of impropers Ni in molecule, default = 0
+* Ng *groups* = # of groups in molecule, default = 0
 * Mtotal *mass* = total mass of molecule
 * Xc Yc Zc *com* = coordinates of center-of-mass of molecule
 * Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
@@ -243,6 +244,20 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.
 ----------
 
 
+*Groups* section:
+
+* one line per group
+* line syntax: ID a b c d ...
+* a,b,c,d,... = IDs of atoms in group
+
+The ID of a group can only contain alphanumeric characters and
+underscores.  The atom IDs should be values from 1 to Natoms, where
+Natoms = # of atoms in the molecule.
+
+
+----------
+
+
 *Charges* section:
 
 * one line per atom

src/molecule.h

@@ -379,6 +379,10 @@ E: Invalid Molecules section in molecule file
 
 Self-explanatory.
 
+E: Invalid atom ID in Groups section of molecule file
+
+Self-explanatory.
+
 E: Invalid Special Bond Counts section in molecule file
 
 Self-explanatory.