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Updated docs.

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rohskopf
2022-07-01 21:07:19 -06:00
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doc/src/compute_sna_atom.rst
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@ -464,15 +464,8 @@ gradient components
where :math:`a` is the Cartesian direction for the gradient. The rows are where :math:`a` is the Cartesian direction for the gradient. The rows are
organized in chunks, where each chunk corresponds to an atom :math:`j` in the organized in chunks, where each chunk corresponds to an atom :math:`j` in the
system of :math:`N` atoms. The rows in an atom :math:`j` chunk correspond to system of :math:`N` atoms. The rows in an atom :math:`j` chunk correspond to
atoms :math:`i` that have :math:`j` as a neighbor. The number of rows in the atoms :math:`i` in the system of :math:`N` atoms. The total number of rows for
atom :math:`j` chunk is therefore equal to the number of neighbors these descriptor gradients is therefore :math:`3N^2`.
:math:`N_{neighs}[j]` within the SNAP potential cutoff radius of atom :math:`j`
, times 3 for each Cartesian direction. The total number of rows for these
descriptor gradients is therefore
.. math::
3 \sum_j^{N} N_{neighs}[j].
For *dgradflag=1*, the number of columns is equal to the number of bispectrum components, For *dgradflag=1*, the number of columns is equal to the number of bispectrum components,
plus 3 additional columns representing the indices :math:`i`, :math:`j`, and :math:`a` which plus 3 additional columns representing the indices :math:`i`, :math:`j`, and :math:`a` which
@ -483,8 +476,9 @@ For the descriptor gradient rows, the first 3 columns contain the indices
of different descriptors indexed by :math:`k`. of different descriptors indexed by :math:`k`.
The first 3 columns of the first :math:`N` rows belong to the reference The first 3 columns of the first :math:`N` rows belong to the reference
potential force components. The first column of the last row, after the first potential force components. The first column of the last row, after the first
:math:`N + 3 \sum_j^{N} N_{neighs}[j]` rows, contains the reference potential :math:`N + 3N^2` rows, contains the reference potential
energy. The virial components are not used with this option. energy. The virial components are not used with this option. The total number of
rows is therefore :math:`N + 3N^2 + 1` and the number of columns is :math:`K + 3`.
These values can be accessed by any command that uses per-atom values 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>` doc from a compute as input. See the :doc:`Howto output <Howto_output>` doc