Merge remote-tracking branch 'github/develop' into collected-small-fixes

doc/src/Commands_compute.rst

@@ -118,6 +118,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ptm/atom <compute_ptm_atom>`
    * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
+   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`

doc/src/compute.rst

@@ -282,6 +282,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
 * :doc:`rattlers/atom <compute_rattlers_atom>` - identify under-coordinated rattler atoms
 * :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
+* :doc:`reaxff/atom <compute_reaxff_atom>` - extract ReaxFF bond information
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region

doc/src/compute_reaxff_atom.rst

@@ -0,0 +1,97 @@
+.. index:: compute reaxff/atom
+.. index:: compute reaxff/atom/kk
+
+compute reaxff/atom command
+===========================
+
+Accelerator Variants: *reaxff/atom/kk*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID reaxff/atom attribute args ... keyword value ...
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* reaxff/atom = name of this compute command
+* attribute = *pair*
+
+  .. parsed-literal::
+
+       *pair* args = nsub
+         nsub = *n*-instance of a sub-style, if a pair style is used multiple times in a hybrid style
+
+* keyword = *bonds*
+
+  .. parsed-literal::
+
+       *bonds* value = *no* or *yes*
+         *no* = ignore list of local bonds
+         *yes* = include list of local bonds
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   compute 1 all reaxff/atom bonds yes
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Define a computation that extracts bond information computed by the ReaxFF
+potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
+
+By default, it produces per-atom data that includes the following columns:
+
+* abo = atom bond order (sum of all bonds)
+* nlp = number of lone pairs
+* nb = number of bonds
+
+Bonds will only be included if its atoms are in the group.
+
+In addition, if ``bonds`` is set to ``yes``, the compute will also produce a
+local array of all bonds on the current processor whose atoms are in the group.
+The columns of each entry of this local array are:
+
+* id_i = atom i id of bond
+* id_j = atom j id of bond
+* bo = bond order of bond
+
+Output info
+"""""""""""
+
+This compute calculates a per-atom array and local array depending on the
+number of keywords. The number of rows in the local array is the number of
+bonds as described above. Both per-atom and local array have 3 columns.
+
+The arrays can be accessed by any command that uses local and per-atom values
+from a compute as input.  See the :doc:`Howto output <Howto_output>` page for
+an overview of LAMMPS output options.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Restrictions
+""""""""""""
+
+The compute reaxff/atom command requires that the :doc:`pair_style reaxff
+<pair_reaxff>` is invoked.  This fix is part of the REAXFF package.  It is only
+enabled if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style reaxff <pair_reaxff>`
+
+Default
+"""""""
+
+The option defaults are *bonds* = *no*.

doc/src/compute_stress_mop.rst

@@ -18,7 +18,7 @@ Syntax
 * style = *stress/mop* or *stress/mop/profile*
 * dir = *x* or *y* or *z* is the direction normal to the plane
 * args = argument specific to the compute style
-* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
+* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* or *dihedral* (one or more can be specified)
 
 .. parsed-literal::
 
@@ -68,15 +68,13 @@ Verlet algorithm.
 
 .. versionadded:: 15Jun2023
 
-   contributions from bond and angle potentials
+   contributions from bond, angle and dihedral potentials
 
-Between one and six keywords can be used to indicate which contributions
+Between one and seven keywords can be used to indicate which contributions
 to the stress must be computed: total stress (total), kinetic stress
 (kin), configurational stress (conf), stress due to bond stretching
-(bond), stress due to angle bending (angle) and/or due to pairwise
-non-bonded interactions (pair).  The angle keyword is currently
-available only for the *stress/mop* command and **not** the
-*stress/mop/profile* command.
+(bond), stress due to angle bending (angle), stress due to dihedral terms (dihedral)
+and/or due to pairwise non-bonded interactions (pair).
 
 NOTE 1: The configurational stress is computed considering all pairs of
 atoms where at least one atom belongs to group group-ID.
@@ -134,14 +132,9 @@ size does not change in time, and axis-aligned planes.
 The method only works with two-body pair interactions, because it
 requires the class method ``Pair::single()`` to be implemented, which is
 not possible for manybody potentials.  In particular, compute
-*stress/mop/profile* does not work with more than two-body pair
+*stress/mop/profile* and *stress/mop* do not work with more than two-body pair
 interactions, long range (kspace) interactions and
-angle/dihedral/improper intramolecular interactions. Similarly, compute
-*stress/mop* does not work with more than two-body pair interactions,
-long range (kspace) interactions and dihedral/improper intramolecular
-interactions but works with all bond interactions with the class method
-single() implemented and all angle interactions with the class method
-born_matrix() implemented.
+improper intramolecular interactions.
 
 Related commands
 """"""""""""""""

doc/src/pair_reaxff.rst

@@ -373,7 +373,8 @@ Related commands
 
 :doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
 :doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
-:doc:`fix reaxff/species <fix_reaxff_species>`
+:doc:`fix reaxff/species <fix_reaxff_species>`,
+:doc:`compute reaxff/atom <compute_reaxff_atom>`
 
 Default
 """""""