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small doc fixes

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Axel Kohlmeyer
2024-04-16 19:26:51 -04:00
parent 972d412186
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1 changed files with 31 additions and 29 deletions
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doc/src/pair_mliap.rst
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@ -75,21 +75,23 @@ The available models are *linear* and *nn*.
.. versionadded:: TBD
The descriptor style *ace* is a class of highly general atomic descriptors,
atomic cluster expansion descriptors (ACE) from :ref:`(Drautz) <Drautz19>` ,
that include a radial basis, an angular basis, and bases for other variables
(such as chemical species) if relevant. In descriptor style *ace*, the *ace*
descriptors may be defined up to an arbitrary body order. This descriptor
style is the same as that used in :doc:`pair_style pace <pair_pace>` and
:doc:`compute pace <compute_pace>`. The available models with *ace* in
ML-IAP are *linear* and *mliappy*. The *ace* descriptors and models require
building LAMMPS with the ML-PACE package (see below). The *mliappy* model
style may be used with *ace* descriptors, but it requires that LAMMPS is
also built with the PYTHON package. As with other, the *mliappy* model style
can be used to couple arbitrary python models that use the *ace* descriptors
such as Pytorch NNs. Note that *ALL* mliap model styles with *ace* descriptors
require that descriptors and hyperparameters are supplied in a `.yace` or `.ace`
file, similar to :doc:`compute pace <compute_pace>`.
The descriptor style *ace* is a class of highly general atomic
descriptors, atomic cluster expansion descriptors (ACE) from
:ref:`(Drautz) <Drautz19>`, that include a radial basis, an angular
basis, and bases for other variables (such as chemical species) if
relevant. In descriptor style *ace*, the *ace* descriptors may be
defined up to an arbitrary body order. This descriptor style is the same
as that used in :doc:`pair_style pace <pair_pace>` and :doc:`compute
pace <compute_pace>`. The available models with *ace* in ML-IAP are
*linear* and *mliappy*. The *ace* descriptors and models require
building LAMMPS with the ML-PACE package (see below). The *mliappy*
model style may be used with *ace* descriptors, but it requires that
LAMMPS is also built with the PYTHON package. As with other model
styles, the *mliappy* model style can be used to couple arbitrary python
models that use the *ace* descriptors such as Pytorch NNs. Note that
*ALL* mliap model styles with *ace* descriptors require that descriptors
and hyperparameters are supplied in a `.yace` or `.ace` file, similar to
:doc:`compute pace <compute_pace>`.
The pair_style *mliap* command must be followed by two keywords *model*
and *descriptor* in either order, or the one keyword *unified*. A
@ -201,20 +203,20 @@ of SO3 descriptor and model files can be done with the
The ACE descriptor file differs from the SNAP and SO3 files. It more
closely resembles the potential file format for linear or square-root
embedding ACE potentials used in the :doc:`pair_style pace <pair_pace>`.
As noted above, the key difference is that the Clebsch-Gordan coefficients
in the descriptor file with *mliap descriptor ace* are *NOT* multiplied
multiplied by linear or square root embedding terms. In other words,
the model is separated from the descriptor definitions and
hyperparameters. In :doc:`pair_style pace <pair_pace>`, they are combined.
The ACE descriptor files required by *mliap* are generated automatically
in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_ during linear,
pytorch, etc. ACE model fitting. Additional tools are provided there to
prepare *ace* descriptor files and hyperparameters before model fitting.
The *ace* descriptor files can also be extracted from ACE model fits in
`python-ace. <https://github.com/ICAMS/python-ace>`_ It is important to
note that order of the types listed in :doc:`pair_coeff <pair_coeff>` must
match the order of the elements/types listed in the ACE descriptor file
for all *mliap* styles when using *ace* descriptors.
As noted above, the key difference is that the Clebsch-Gordan
coefficients in the descriptor file with *mliap descriptor ace* are
*NOT* multiplied by linear or square root embedding terms. In other
words,the model is separated from the descriptor definitions and
hyperparameters. In :doc:`pair_style pace <pair_pace>`, they are
combined. The ACE descriptor files required by *mliap* are generated
automatically in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_ during
linear, pytorch, etc. ACE model fitting. Additional tools are provided
there to prepare *ace* descriptor files and hyperparameters before model
fitting. The *ace* descriptor files can also be extracted from ACE
model fits in `python-ace. <https://github.com/ICAMS/python-ace>`_. It
is important to note that order of the types listed in :doc:`pair_coeff
<pair_coeff>` must match the order of the elements/types listed in the
ACE descriptor file for all *mliap* styles when using *ace* descriptors.
See the :doc:`pair_coeff <pair_coeff>` page for alternate ways
to specify the path for these *model* and *descriptor* files.