fix whitespace and minor documentation integration issues
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@ -91,7 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
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* :doc:`ke/atom/eff <compute_ke_atom_eff>`
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* :doc:`ke/eff <compute_ke_eff>`
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* :doc:`ke/rigid <compute_ke_rigid>`
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* :doc:`local/comp/atom <compute_local_comp_atom>`
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* :doc:`local/comp/atom (k) <compute_local_comp_atom>`
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* :doc:`mliap <compute_mliap>`
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* :doc:`momentum <compute_momentum>`
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* :doc:`msd <compute_msd>`
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@ -1,7 +1,10 @@
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.. index:: compute local/comp/atom
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.. index:: compute local/comp/atom/kk
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compute local/comp/atom command
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======================================
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===============================
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Accelerator Variants: *local/comp/atom/kk*
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Syntax
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""""""
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@ -33,7 +36,7 @@ Examples
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Description
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"""""""""""
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.. versionadded:: 24May2023
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.. versionadded:: TBD
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Define a computation that calculates a local composition vector for each
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atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,
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@ -43,14 +46,14 @@ the sum of all compositions equals one.
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.. note::
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This compute uses the number of atom types, not chemical species, assigned in
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:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
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species (i.e., Cu and Ni) assigned to four different atom types in
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:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
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output four fractional values. In those cases, the user may desire an extra
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calculation step to consolidate per-type fractions into per-species fractions.
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This calculation can be conducted within LAMMPS using another compute such as
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:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
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This compute uses the number of atom types, not chemical species, assigned in
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:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
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species (i.e., Cu and Ni) assigned to four different atom types in
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:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
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output four fractional values. In those cases, the user may desire an extra
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calculation step to consolidate per-type fractions into per-species fractions.
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This calculation can be conducted within LAMMPS using another compute such as
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:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
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post-processing step.
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----------
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@ -91,7 +94,7 @@ Output info
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This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N`
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is the number of atom types. The first column is a count of the number of atoms
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used to calculate composition (including the central atom), and each subsequent
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column indicates the fraction of that atom type within the cutoff sphere.
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column indicates the fraction of that atom type within the cutoff sphere.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See the :doc:`Howto output <Howto_output>`
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@ -198,7 +198,7 @@ void ComputeLocalCompAtom::compute_peratom()
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double lfac = 1.0 / count;
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for (int n = 1; n < size_peratom_cols; n++)
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result[i][n+1] *= lfac;
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}
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}
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}
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