Installation and Setup
======================

Dependencies
------------

Versions indicated are those used during development. Other versions may be
compatible, but have not yet been tested.

  * `SciPy 1.0.1 <https://www.scipy.org/install.html>`_
  * `NumPy 1.14.3 <https://www.scipy.org/scipylib/download.html>`_
  * `Pandas 0.20.3 <https://pandas.pydata.org/getpandas.html>`_
  * `Pymatgen 2017.9.3 <http://pymatgen.org/#getting-pymatgen>`_
  * `SpgLib for Python 1.9.9.44 <https://atztogo.github.io/spglib/python-spglib.html#installation>`_
  * `Openbabel 2.4.1 <http://openbabel.org/wiki/Category:Installation>`_
  * `Networkx 2.3 <https://networkx.github.io>`_

Openbabel is not necessary, and only adds additional file format support for
importing molecules. You must install the C++ pacakge before installing the
Python bindings. For Debian based systems, your distribution may already have
installable packages:

::

    $ sudo apt-get install openbabel
    $ pip install openbabel

Also note that the openbabel Python bindings require swig to install:

::

    $ sudo apt-get install swig

Older version of swig (before 2.0) will not work. For other systems, you must
compile the openbabel Python bindings yourself. There are tutorials for this on
the `openbabel website
<https://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html>`_, as well as
in the `pymatgen documentation
<http://pymatgen.org/installation.html#openbabel-mac-os-x-tested-on-v2-3-2>`_.

Installation
------------

To install PxXtal, one can simply type

::

    $ pip install pyxtal

or make a copy of the source code, and then install it manually.

::

    $ git clone https://github.com/MaterSim/pyxtal
    $ cd pyxtal
    $ pip install .


or update the code to our developing version

::

    $ pip install --upgrade git+https://github.com/MaterSim/PyXtal.git@master


This will install the module. You can check the installation of the code by a
simple test run as follows,

::

    $ pyxtal_test.py

You expect to see the following output.

::

                ______       _    _          _
                (_____ \     \ \  / /        | |
                 _____) )   _ \ \/ / |_  ____| |
                |  ____/ | | | )  (|  _)/ _  | |
                | |    | |_| |/ /\ \ |_( ( | | |___
                |_|     \__  /_/  \_\___)_||_|_(___
                       (____/


    ----------------------(version 0.0.1 )----------------------

    A Python package for random crystal generation
    The source code is available at https://github.com/MaterSim/pyxtal
    Developed by Zhu's group at University of Nevada Las Vegas


    ====== Testing functionality for pyXtal version 0.1dev ======
    Importing sys...
    Success!
    Importing numpy...
    Success!
    Importing pymatgen...
    Success!
    Importing pandas...
    Success!
    ...
    ...
    	223	|	223	|	223	|	1.12 s ~
    	224	|	224	|	224	|	0.30 s
    	225	|	225	|	225	|	0.54 s
    	226	|	226	|	226	|	0.45 s
    	227	|	227	|	227	|	0.47 s
    	228	|	228	|	228	|	1.42 s ~
    	229	|	229	|	229	|	0.19 s
    	230	|	230	|	230	|	0.18 s
    TEST COMPLETE

    Total time elapsed: 34.15 s

More extensive test can be invoked by running

::

    $ pyxtal_test.py -m all

Ideally, one should see the completion of all modules in the end.