Chimie Théorique » scripts_chimie4psmn » DockOnSurf

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	set SPHINXBUILD=sphinx-build

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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.

# 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 -------------------------------------------------

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# 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']

Contact/Contribute

==================

FAQs

====

.. 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`

Input file reference manual

===========================

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>`_.

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.

Release notes

=============

Tips and tricks

===============

Tutorials

=========

Getting started

^^^^^^^^^^^^^^^