fix whitespace and minor documentation integration issues

This commit is contained in:
Axel Kohlmeyer
2023-08-04 21:06:47 -04:00
parent 4c68e3f5f3
commit 5e9658aff6
3 changed files with 16 additions and 13 deletions

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@ -91,7 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`local/comp/atom <compute_local_comp_atom>`
* :doc:`local/comp/atom (k) <compute_local_comp_atom>`
* :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`

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@ -1,7 +1,10 @@
.. index:: compute local/comp/atom
.. index:: compute local/comp/atom/kk
compute local/comp/atom command
======================================
===============================
Accelerator Variants: *local/comp/atom/kk*
Syntax
""""""
@ -33,7 +36,7 @@ Examples
Description
"""""""""""
.. versionadded:: 24May2023
.. versionadded:: TBD
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,
@ -43,14 +46,14 @@ the sum of all compositions equals one.
.. note::
This compute uses the number of atom types, not chemical species, assigned in
:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
species (i.e., Cu and Ni) assigned to four different atom types in
:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
output four fractional values. In those cases, the user may desire an extra
calculation step to consolidate per-type fractions into per-species fractions.
This calculation can be conducted within LAMMPS using another compute such as
:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
This compute uses the number of atom types, not chemical species, assigned in
:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
species (i.e., Cu and Ni) assigned to four different atom types in
:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
output four fractional values. In those cases, the user may desire an extra
calculation step to consolidate per-type fractions into per-species fractions.
This calculation can be conducted within LAMMPS using another compute such as
:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
post-processing step.
----------
@ -91,7 +94,7 @@ Output info
This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N`
is the number of atom types. The first column is a count of the number of atoms
used to calculate composition (including the central atom), and each subsequent
column indicates the fraction of that atom type within the cutoff sphere.
column indicates the fraction of that atom type within the cutoff sphere.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>`

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@ -198,7 +198,7 @@ void ComputeLocalCompAtom::compute_peratom()
double lfac = 1.0 / count;
for (int n = 1; n < size_peratom_cols; n++)
result[i][n+1] *= lfac;
}
}
}