commit 4fd2e6f02ea63b43d2ac5fc482257d9659418bf3
Author: Carles Martí <carles.marti2@gmail.com>
Date:   Thu Feb 11 23:51:42 2021 +0100

    Added documentation files.

diff --git a/.gitignore b/.gitignore
index 8cd1c43..e096a64 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,4 @@ __pycache__
 .idea
 dockonsurf.log
 *.nfs*
+docs/build/*
\ No newline at end of file
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d0c3cbf
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..6247f7e
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/about.rst b/docs/source/about.rst
new file mode 100644
index 0000000..7c679a3
--- /dev/null
+++ b/docs/source/about.rst
@@ -0,0 +1,32 @@
+About
+=====
+
+DockOnSurf is a program to automatically find the most stable geometry for molecules
+on surfaces.
+
+webpage: https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf
+
+Features
+^^^^^^^^
+* Generate a handful of adsorbate-surface structures by 
+  combining:
+  * surface sites
+  * adsorbate's anchoring points
+  * conformers
+  * orientations
+  * probe dissociation of acidic H
+  
+* Guess the direction where to place the adsorbate. 
+  Useful for nanoparticles or stepped/kinked surfaces.
+  
+* Sample different orientations efficiently by using internal angles.
+
+* Detect and correct atomic clashes.
+
+* Optimize the geometry of the generated structures using CP2K or VASP.
+  
+* Submit jobs to your computing center and check if they have finished normally.
+
+* Track progress by logging all events on a log file.
+
+* Customize the execution by changing chemically meaningful  the edition of a simple input file.
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000..6c27f94
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,55 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'DockOnSurf'
+copyright = '2021, Carles Martí'
+author = 'Carles Martí'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
diff --git a/docs/source/contact.rst b/docs/source/contact.rst
new file mode 100644
index 0000000..43f1097
--- /dev/null
+++ b/docs/source/contact.rst
@@ -0,0 +1,2 @@
+Contact/Contribute
+==================
diff --git a/docs/source/faqs.rst b/docs/source/faqs.rst
new file mode 100644
index 0000000..144696f
--- /dev/null
+++ b/docs/source/faqs.rst
@@ -0,0 +1,2 @@
+FAQs
+====
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000..771e1ee
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,59 @@
+.. DockOnSurf documentation master file, created by
+   sphinx-quickstart on Thu Feb 11 20:09:40 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+DockOnSurf
+==========
+
+DockOnSurf is a program to automatically find the most stable geometry for molecules
+on surfaces.
+
+Features
+^^^^^^^^
+* Generate a handful of adsorbate-surface structures by combining:
+
+  * surface sites
+  * adsorbate's anchoring points
+  * conformers
+  * orientations
+  * probe dissociation of acidic H
+
+* Guess the direction where to place the adsorbate.
+  Useful for nanoparticles or stepped/kinked surfaces.
+
+* Sample different orientations efficiently by using internal angles.
+
+* Detect and correct atomic clashes.
+
+* Optimize the geometry of the generated structures using CP2K or VASP.
+
+* Submit jobs to your computing center and check if they have finished normally.
+
+* Track progress by logging all events on a log file.
+
+* Customize the execution by changing chemically meaningful  the edition of a simple input file. DockOnSurf is a program to automatically find the most stable geometry for molecules on surfaces.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents
+
+   about
+   installation
+   tutorials
+   inp_ref_manual
+   tips_and_tricks
+   faqs
+   release_notes
+   contact
+   license
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/inp_ref_manual.rst b/docs/source/inp_ref_manual.rst
new file mode 100644
index 0000000..6a74696
--- /dev/null
+++ b/docs/source/inp_ref_manual.rst
@@ -0,0 +1,2 @@
+Input file reference manual
+===========================
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
new file mode 100644
index 0000000..ca8aa1d
--- /dev/null
+++ b/docs/source/installation.rst
@@ -0,0 +1,40 @@
+Installation
+============
+Download the ``dockonsurf`` directory and place it somewhere in your computer,
+by typing in your terminal: ::
+
+    git clone http://forge.cbp.ens-lyon.fr/git/dockonsurf
+
+In order to be able to execute DockOnSurf by simply typing ``dockonsurf.py`` You need 
+to add the DockOnSurf directory in your ``PATH``. Assuming you download it in your ``$HOME``
+directory, add ``$HOME/dockonsurf`` to your ``PATH`` variable by typing: ::
+
+    PATH="$PATH:$HOME/dockonsurf/"
+
+If you downloaded it elsewhere, replace ``$HOME`` for the actual path where your DockOnSurf is 
+(where you did the ``git clone`` command).
+If you want to permanently add the DockOnSurf directory in your ``PATH`` add 
+``PATH="$PATH:$HOME/dockonsurf/"`` at the end of your ``$HOME/.bashrc`` file.
+
+DockOnSurf needs the python libraries listed under **Requirements** to be installed 
+and available. The easiest way to do this is with the ``conda`` package and environment 
+manager (see https://docs.conda.io/en/latest/). You can alternatively install 
+them using pip except from RDKit, which is not available as its core routines are 
+written in C.
+
+Requirements
+^^^^^^^^^^^^
+
+* `Python <http://www.python.org/>`_ >= 3.6
+* `Matplotlib <https://matplotlib.org>`_ ~= 3.2.1
+* `NumPy <http://docs.scipy.org/doc/numpy/reference/>`_ >= 1.16.6
+* `RDKit <https://rdkit.org/>`_ ~= 2019.9.3
+* `scikit-learn <https://scikit-learn.org/>`_ ~= 0.23.1
+* `HDBSCAN <https://hdbscan.readthedocs.io/en/latest/basic_hdbscan.html>`_ ~= 0.8.26
+* `ASE <https://wiki.fysik.dtu.dk/ase/>`_ ~= 3.19.1
+* `NetworkX <https://networkx.org/>`_ >= 2.4
+* `python-daemon <https://pypi.org/project/python-daemon/>`_ ~= 2.2.4
+* `pymatgen <https://pymatgen.org/>`_ ~= 2020.11.11
+* `pycp2k <https://github.com/SINGROUP/pycp2k>`_ ~= 0.2.2
+
+For instance, `this is a hyperlink reference <https://odoo.com>`_.
diff --git a/docs/source/license.rst b/docs/source/license.rst
new file mode 100644
index 0000000..bb9645f
--- /dev/null
+++ b/docs/source/license.rst
@@ -0,0 +1,13 @@
+License
+=======
+
+The MIT License (MIT)
+
+Copyright © 2020 Centre National de la Recherche Scientifique <http://www.cnrs.fr/>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
new file mode 100644
index 0000000..352cc6a
--- /dev/null
+++ b/docs/source/release_notes.rst
@@ -0,0 +1,2 @@
+Release notes
+=============
diff --git a/docs/source/tips_and_tricks.rst b/docs/source/tips_and_tricks.rst
new file mode 100644
index 0000000..e9254e2
--- /dev/null
+++ b/docs/source/tips_and_tricks.rst
@@ -0,0 +1,2 @@
+Tips and tricks
+===============
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
new file mode 100644
index 0000000..55cffe5
--- /dev/null
+++ b/docs/source/tutorials.rst
@@ -0,0 +1,5 @@
+Tutorials
+=========
+
+Getting started
+^^^^^^^^^^^^^^^
