Merge remote-tracking branch 'origin/master'

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)
 

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 %
+   :scale: 60 %

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/
+.. _VESTA: https://jp-minerals.org/vesta/en/