Metadata-Version: 1.2
Name: CatKit
Version: 0.3.0
Summary: General purpose tools for high-throughput catalysis.
Home-page: https://github.com/SUNCAT-Center/CatKit
Author: Jacob Boes
Author-email: jrboes@stanford.edu
License: GPL-3.0
Description: #+Title: CatKit: Catalysis Kit
        #+Author: SUNCAT Method Development Team
        #+OPTIONS: toc:nil
        
        #+BEGIN_HTML
        <a href='https://travis-ci.org/SUNCAT-Center/CatKit.svg?branch=master'><img src='https://travis-ci.org/SUNCAT-Center/CatKit.svg?branch=master'/></a>
        <a href='https://coveralls.io/github/SUNCAT-Center/CatKit?branch=master'><img src='https://coveralls.io/repos/github/SUNCAT-Center/CatKit/badge.svg?branch=master' alt='Coverage Status' /></a>
        #+END_HTML
        
        Welcome to CatKit! A staging ground for computational tools which are generally useful for catalysis research. The goal of the project is to provide a communal location for those interested in hosting such tools under a common banner. In doing so, we hope to provide the infrastructure to produce more advanced functionality based on modular components of individual contributors.
        
        * Graph-atoms (Gratoms) object
        The =Gratoms= object is a child class of the ASE =Atoms= object class. Effectively, this means that it has all the same functionality as an =Atoms= object with some additional features as well.
        
        ** Graph information
        The =Gratoms= object primary function is to conveniently store and manage graph information.
        
        #+BEGIN_SRC python :results output org drawer
        from catkit import Gratoms
        from catgen.molecules import get_topologies
        
        atoms0 = get_topologies('C4', saturate=True)[0]
        
        print(type(atoms0))
        print('\nAtomic numbers:\n{}\n'.format(atoms0.numbers))
        print('Connectivity matrix:\n{}'.format(atoms0.connectivity))
        
        atoms1 = atoms0.copy()
        del atoms1[0]
        
        print('\nAtomic numbers:\n{}\n'.format(atoms1.numbers))
        print('Connectivity matrix:\n{}'.format(atoms1.connectivity))
        print('\nAre isomorphs: {}'.format(atoms0.is_isomorph(atoms1)))
        
        atoms2 = atoms1 + Gratoms('C')
        
        print('\nAtomic numbers:\n{}\n'.format(atoms2.numbers))
        print('Connectivity matrix:\n{}'.format(atoms2.connectivity))
        
        atoms2.graph.add_edges_from([(0, 13), (1, 13), (2, 13), (3, 13)])
        
        print('\nAtomic numbers:\n{}\n'.format(atoms2.numbers))
        print('Connectivity matrix:\n{}'.format(atoms2.connectivity))
        
        print('\nAre isomorphs: {}'.format(atoms0.is_isomorph(atoms2)))
        #+END_SRC
        
        #+RESULTS:
        :RESULTS:
        <class 'catkit.gratoms.Gratoms'>
        
        Atomic numbers:
        [6 6 6 6 1 1 1 1 1 1 1 1 1 1]
        
        Connectivity matrix:
        [[0 1 1 1 1 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 1 1 1 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 1 1 1 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 1 1 1]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 0 1 0 0 0 0 0 0 0 0 0 0]
         [0 0 0 1 0 0 0 0 0 0 0 0 0 0]
         [0 0 0 1 0 0 0 0 0 0 0 0 0 0]]
        
        Atomic numbers:
        [6 6 6 1 1 1 1 1 1 1 1 1 1]
        
        Connectivity matrix:
        [[0 0 0 0 1 1 1 0 0 0 0 0 0]
         [0 0 0 0 0 0 0 1 1 1 0 0 0]
         [0 0 0 0 0 0 0 0 0 0 1 1 1]
         [0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0]]
        
        Are isomorphs: False
        
        Atomic numbers:
        [6 6 6 1 1 1 1 1 1 1 1 1 1 6]
        
        Connectivity matrix:
        [[0 0 0 0 1 1 1 0 0 0 0 0 0 0]
         [0 0 0 0 0 0 0 1 1 1 0 0 0 0]
         [0 0 0 0 0 0 0 0 0 0 1 1 1 0]
         [0 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 0 0 0 0 0 0 0 0 0 0 0 0]]
        
        Atomic numbers:
        [6 6 6 1 1 1 1 1 1 1 1 1 1 6]
        
        Connectivity matrix:
        [[0 0 0 0 1 1 1 0 0 0 0 0 0 1]
         [0 0 0 0 0 0 0 1 1 1 0 0 0 1]
         [0 0 0 0 0 0 0 0 0 0 1 1 1 1]
         [0 0 0 0 0 0 0 0 0 0 0 0 0 1]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [1 0 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 1 0 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [0 0 1 0 0 0 0 0 0 0 0 0 0 0]
         [1 1 1 1 0 0 0 0 0 0 0 0 0 0]]
        
        Are isomorphs: True
        :END:
        
        * CatGen: Catalysis Generator
        CatGen is an enumeration module designed to construct various catalytic structures.
        
        - [X] Gas phase molecules
        - [ ] Bulk structures
        - [X] Surfaces structures
        - [X] Adsorption sites
        - [X] Catalytic structures
        
        It also has functionality for enumeration of other systems relevant to the field of catalysis.
        
        - [X] Reaction mechanisms
        - [X] Reaction routes
        
        For additional details regarding how the generator operates, including example usage, see the [[./catgen/readme.org][CatGen readme]].
        
        * CatFlow: Catalysis Workflow
        CatFlow is currently a staging ground for Workflow code and techniques. These functions are meant to be used in conjunction with the other modules inside CatKit to help automate these tasks.
        
        Currently, CatFlow's functionality utilizes [[https://materialsproject.github.io/fireworks/][Fireworks]] and many of the functions are also specifically tailored to work on the high-performance computers which are available to the [[http://suncat.stanford.edu/][SUNCAT]] group as Stanford.
        
        For additional detail see the [[./catflow/readme.org][CatFlow readme]].
        
        * Dependencies
        CatKit attempts to make use of basic functionalities implemented by existing softwares when possible to extend its capabilities.
        
        A full list of required packaged can be found in [[./requirements.txt][the requirements]].
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4
