From fe0541fde7439f7f2fa5d224da681e54848da372 Mon Sep 17 00:00:00 2001 From: rohskopf Date: Fri, 16 Sep 2022 17:41:05 -0600 Subject: [PATCH] End rst doc files with transition --- doc/src/compute_podfit.rst | 25 ++++++------------------- doc/src/pair_pod.rst | 24 ++++++------------------ 2 files changed, 12 insertions(+), 37 deletions(-) diff --git a/doc/src/compute_podfit.rst b/doc/src/compute_podfit.rst index de383d20af..2899708100 100644 --- a/doc/src/compute_podfit.rst +++ b/doc/src/compute_podfit.rst @@ -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) ` 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) ` +mathematical definition is given in :ref:`(Nguyen) ` 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). \ No newline at end of file diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst index 544bd727ed..d444af18a9 100644 --- a/doc/src/pair_pod.rst +++ b/doc/src/pair_pod.rst @@ -21,10 +21,10 @@ Examples Description """"""""""" -Pair style *pod* defines the proper orthogonal descriptor (POD) potential, -:ref:`(Thompson) `. The mathematical definition of the POD potential -is described from :doc:`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 `, 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) ` 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). \ No newline at end of file