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End rst doc files with transition

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rohskopf
2022-09-16 17:41:05 -06:00
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25
doc/src/compute_podfit.rst
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@ -127,9 +127,9 @@ fitted potentials. When fitting the same functional form on *Q* different data s
obtain *Q* different optimized potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu_q^*), 1 \le q \le Q`.
Consequently, there exist many different sets of optimized parameters for empirical interatomic potentials.
Instead of optimizing the potential parameters, inspired by the reduced basis method
:ref:`(Thompson) <Thompson20141>` for parametrized partial differential equations,
we view the parametrized PES as a parametric manifold of potential energies
Instead of optimizing the potential parameters, inspired by the reduced basis method for
parametrized partial differential equations, we view the parametrized PES as a parametric manifold
of potential energies.
.. math::
@ -151,8 +151,7 @@ Proper Orthogonal Descriptors
Proper orthogonal descriptors are finger prints characterizing the
radial and angular distribution of a system of atoms. The detailed
mathematical definition is given in the paper by Nguyen et
al. :ref:`(Thompson) <Thompson20141>`
mathematical definition is given in :ref:`(Nguyen) <Nguyen2022>`
The descriptors for the one-body interaction are used to captured energy of isolated elements and defined as follows
@ -660,18 +659,6 @@ The keyword defaults are also given in the description of the input files.
----------
.. _Thompson20142:
.. _Nguyen2022:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).
.. _Bartok20102:
**(Bartok2010)** Bartok, Payne, Kondor, Csanyi, Phys Rev Lett, 104, 136403 (2010).
.. _Wood20182:
**(Wood)** Wood and Thompson, J Chem Phys, 148, 241721, (2018)
.. _Cusentino20202:
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
**(Nguyen)** Ngueyn, et. al., arxiv (2022).

24
doc/src/pair_pod.rst
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@ -21,10 +21,10 @@ Examples
Description
"""""""""""
Pair style *pod* defines the proper orthogonal descriptor (POD) potential,
:ref:`(Thompson) <Thompson20142>`. The mathematical definition of the POD potential
is described from :doc:`compute podfit <compute_podfit>`, which is used to fit the POD
potential to *ab initio* energy and force data.
Pair style *pod* defines the proper orthogonal descriptor (POD) potential. The mathematical
definition of the POD potential is described from :doc:`compute podfit <compute_podfit>`, which is
used to fit the POD potential to *ab initio* energy and force data. More details on the POD potential
are given in :ref:`(Nguyen) <Nguyen2022>`
Only a single pair_coeff command is used with the *pod* style which
specifies a POD parameter file followed by a coefficient file.
@ -64,18 +64,6 @@ none
----------
.. _Thompson20142:
.. _Nguyen2022:
**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).
.. _Bartok20102:
**(Bartok2010)** Bartok, Payne, Kondor, Csanyi, Phys Rev Lett, 104, 136403 (2010).
.. _Wood20182:
**(Wood)** Wood and Thompson, J Chem Phys, 148, 241721, (2018)
.. _Cusentino20202:
**(Cusentino)** Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
**(Nguyen)** Ngueyn, et. al., arxiv (2022).