diff --git a/README.md b/README.md index f298e18..510851e 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ A.S. Rosen, J.M. Notestein, R.Q. Snurr. "Identifying Promising Metal-Organic Fra [![DOI](https://zenodo.org/badge/127307047.svg)](https://zenodo.org/badge/latestdoi/127307047) [![Build Status](https://travis-ci.com/arosen93/mof-adsorbate-initializer.svg?branch=master)](https://travis-ci.com/arosen93/mof-adsorbate-initializer) +[![Documentation Status](https://readthedocs.org/projects/mai/badge/?version=latest)](https://mai.readthedocs.io/en/latest/?badge=latest) ![TOC](toc.png) diff --git a/docs/advanced.rst b/docs/advanced.rst index f701d08..1ff567f 100644 --- a/docs/advanced.rst +++ b/docs/advanced.rst @@ -16,7 +16,7 @@ There are a few changes we've made to the usual workflow. The first is that we n -------------------- Neighbor Algorithms -------------------- -When specifying ``site_idx``, the :func:`~mai.adsorbate_constructor.adsorbate_constructor.get_adsorbate` function will automatically use Pymatgen's built-in nearest neighbor algorithms to determine the atoms in the first coordination sphere of the adsorption site. By default, MAI uses Pymatgen's ``crystal`` algorithm, but additional algorithms are available as listed in :func:`~mai.NN_algos.get_NNs_pm` and described here_. Through iterative testing, we have found ``crystal`` to be the best-performing algorithm for MOFs in general, but other algorithms can be considered if desired. +When specifying ``site_idx``, the :func:`~mai.adsorbate_constructor.adsorbate_constructor.get_adsorbate` function will automatically use Pymatgen's built-in nearest neighbor algorithms to determine the atoms in the first coordination sphere of the adsorption site. By default, MAI uses Pymatgen's ``crystalNN`` algorithm, but additional algorithms are available as listed in :func:`~mai.NN_algos.get_NNs_pm` and described here_. Through iterative testing, we have found ``crystalNN`` to be the best-performing algorithm for MOFs in general, but other algorithms can be considered if desired. ---------------------------- Pre-specification of Indices @@ -27,4 +27,4 @@ In addition to the ``site_idx`` keyword in the :func:`~mai.adsorbate_constructor .. |all_H2O| image:: _static/all_H2O.png :align: middle - :scale: 60 % \ No newline at end of file + :scale: 60 % diff --git a/docs/monatomics.rst b/docs/monatomics.rst index f0e6780..766a391 100644 --- a/docs/monatomics.rst +++ b/docs/monatomics.rst @@ -5,7 +5,7 @@ In this example, we'll work through how to add a single atom adsorbate to open m |Cu-BTC| -The metal (Cu) sites here are shown in orange. There are multiple Cu sites per unit cell, and each Cu site is in a paddlewheel-like structure. For this example, we will consider the initialization of an O atom adsorbate to a single coordinatively unsaturated Cu site. +The metal (Cu) sites here are shown in blue. There are multiple Cu sites per unit cell, and each Cu site is in a paddlewheel-like structure. For this example, we will consider the initialization of an O atom adsorbate to a single coordinatively unsaturated Cu site. .. |Cu-BTC| image:: _static/cubtc1.png :align: middle @@ -38,4 +38,4 @@ That concludes our tutorial with monatomic adsorbates. Join me as we move onto m :scale: 25 % .. _inspect: https://wiki.fysik.dtu.dk/ase/ase/atoms.html .. _visualize: https://wiki.fysik.dtu.dk/ase/ase/visualize/visualize.html -.. _VESTA: https://jp-minerals.org/vesta/en/ \ No newline at end of file +.. _VESTA: https://jp-minerals.org/vesta/en/