Merge pull request #1913 from jrgissing/molecule_template_moleculeIDs

Molecule template: molecule-IDs and fragments

doc/src/Errors_messages.rst

@@ -4724,6 +4724,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Invalid Masses section in molecule file*
    Self-explanatory.
 
+*Invalid molecule ID in molecule file*
+   Molecule ID must be a non-zero positive integer.
+
+*Invalid Molecules section in molecule file*
+   Self-explanatory.
+
 *Invalid REAX atom type*
    There is a mis-match between LAMMPS atom types and the elements
    listed in the ReaxFF force field file.
@@ -4790,6 +4796,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Atom IDs must be positive integers and within range of defined
    atoms.
 
+*Invalid atom ID in Fragments 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

@@ -60,6 +60,7 @@ templates include:
 * :doc:`fix rigid/small <fix_rigid>`
 * :doc:`fix shake <fix_shake>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix bond/react <fix_bond_react>`
 * :doc:`create_atoms <create_atoms>`
 * :doc:`atom_style template <atom_style>`
 
@@ -144,6 +145,7 @@ 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
+* Nf *fragments* = # of fragments 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
@@ -166,7 +168,7 @@ internally.
 
 These are the allowed section keywords for the body of the file.
 
-* *Coords, Types, Charges, Diameters, Masses* = atom-property sections
+* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
 * *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
 * *Special Bond Counts, Special Bonds* = special neighbor info
 * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@@ -223,6 +225,26 @@ listed in order from 1 to Nlines, but LAMMPS does not check for this.
 
 ----------
 
+*Molecules* section:
+
+* one line per atom
+* line syntax: ID molecule-ID
+* molecule-ID = molecule ID of atom
+
+----------
+
+*Fragments* section:
+
+* one line per fragment
+* line syntax: ID a b c d ...
+* a,b,c,d,... = IDs of atoms in fragment
+
+The ID of a fragment 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