doc page for new command

doc/src/Commands_compute.rst

@@ -46,6 +46,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
    * :doc:`coord/atom (k) <compute_coord_atom>`
+   * :doc:`count/type <compute_count_type>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`

doc/src/bond_style.rst

@@ -32,13 +32,13 @@ Set the formula(s) LAMMPS uses to compute bond interactions between
 pairs of atoms.  In LAMMPS, a bond differs from a pairwise
 interaction, which are set via the :doc:`pair_style <pair_style>`
 command.  Bonds are defined between specified pairs of atoms and
-remain in force for the duration of the simulation (unless the bond
-breaks which is possible in some bond potentials).  The list of bonded
-atoms is read in by a :doc:`read_data <read_data>` or
-:doc:`read_restart <read_restart>` command from a data or restart file.
-By contrast, pair potentials are typically defined between all pairs
-of atoms within a cutoff distance and the set of active interactions
-changes over time.
+remain in force for the duration of the simulation (unless new bonds
+are created or existing bonds break, which is possible in some fixes
+and bond potentials).  The list of bonded atoms is read in by a
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+command from a data or restart file.  By contrast, pair potentials are
+typically defined between all pairs of atoms within a cutoff distance
+and the set of active interactions changes over time.
 
 Hybrid models where bonds are computed using different bond potentials
 can be setup using the *hybrid* bond style.

doc/src/compute.rst

@@ -200,6 +200,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`com/chunk <compute_com_chunk>` - center of mass for each chunk
 * :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
 * :doc:`coord/atom <compute_coord_atom>` - coordination number for each atom
+* :doc:`count/type <compute_count_type>` - count of atoms or bonds by type
 * :doc:`damage/atom <compute_damage_atom>` - Peridynamic damage for each atom
 * :doc:`dihedral <compute_dihedral>` - energy of each dihedral sub-style
 * :doc:`dihedral/local <compute_dihedral_local>` - angle of each dihedral

doc/src/compute_count_type.rst

@@ -0,0 +1,89 @@
+.. index:: compute count/type
+
+compute count/type command
+====================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID count/type mode
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* count/type = style name of this compute command
+* mode = {atom} or {bond}
+  
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all count/type atom
+   compute 1 flowmols count/type bond
+
+Description
+"""""""""""
+
+Define a computation that counts the current number of atoms by atom
+type or the number of bonds by bond type.  The latter can be useful in
+reactive simulations where bonds are broken or created.
+
+Note that for this command, bonds are the topological kind enumerated
+in a data file, initially read by the :doc:`read_data <read_data>`
+command.  They do not refer to bonds defined on-the-fly by bond-order
+or reactive pair styles.
+
+These commands can create and break toplogical bonds:
+
+* :doc:`fix bond/react <fix_bond_react>`
+* :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/break <fix_bond_break>`
+* :doc:`bond_style quartic <bond_quartic>`
+* :doc:`BPM package <Howto_bpm>` bond styles
+
+If the {mode} setting is {atom} then the count of atoms for each atom
+type is tallied.  Only atoms in the specified group are counted.
+
+If the {mode} setting is {bond} then the count of bonds for each bond
+type is tallied.  Only bonds with both atoms in the specified group
+are counted.
+
+For {mode} = {bond}, broken bonds with a bond type or zero are also
+counted.  Some commands flag broken bonds by setting their bond type
+to zero.  See the :doc:`Howto broken bonds <Howto_broken_bonds>` doc
+page for details.  Note that the group setting is ignored for broken
+bonds; all broken bonds in the system are counted.
+
+----------
+
+Output info
+"""""""""""
+
+This compute calculates a global vector of counts.  If the mode is
+{atom}, the vector length is the number of atom types.  If the mode is
+{bond}, the vector length is the number of bond types.
+
+If the mode is {bond} this compute also calculates a global scalar which
+counts the number of broken bonds.
+
+These values can be used by any command that uses global scalar or
+vector values from a compute as input.  See the :doc:`Howto output
+<Howto_output>` page for an overview of LAMMPS output options.
+
+The scalar and vector values calculated by this compute are "extensive".
+
+Restrictions
+""""""""""""
+
+none
+
+Related commands
+""""""""""""""""
+
+none
+
+Default
+"""""""
+
+none

src/compute_count_type.cpp

@@ -83,6 +83,8 @@ double ComputeCountType::compute_scalar()
   int nbond;
   int count = 0;
 
+  // NOTE: respect group setting
+  
   for (int i = 0; i < nlocal; i++) {
     nbond = num_bond[i];
     for (int m = 0; m < nbond; m++)
@@ -113,6 +115,8 @@ void ComputeCountType::compute_vector()
 
   // count atoms by type
 
+  // NOTE: respect group setting
+
   if (mode == ATOM) {
     int *type = atom->type;
     int nlocal = atom->nlocal;
@@ -128,6 +132,8 @@ void ComputeCountType::compute_vector()
   // skip type = 0 bonds, they are counted by compute_scalar
   // bond types can be negative for SHAKE
 
+  // NOTE: respect group setting
+
   else if (mode == BOND) {
     int *num_bond = atom->num_bond;
     int **bond_type = atom->bond_type;