Metadata-Version: 2.1
Name: aiida-zeopp
Version: 1.0.0a1
Summary: AiiDA plugin for zeo++
Home-page: https://github.com/ltalirz/aiida-zeopp
Author: Leopold Talirz
Author-email: leopold.talirz@epfl.ch
License: Creative Commons
Description: [![Build Status](https://travis-ci.org/ltalirz/aiida-zeopp.svg?branch=master)](https://travis-ci.org/ltalirz/aiida-zeopp)
        [![Coverage Status](https://coveralls.io/repos/github/ltalirz/aiida-zeopp/badge.svg?branch=master)](https://coveralls.io/github/ltalirz/aiida-zeopp?branch=master)
        [![Docs status](https://readthedocs.org/projects/aiida-zeopp/badge)](http://aiida-zeopp.readthedocs.io/)
        [![PyPI version](https://badge.fury.io/py/aiida-zeopp.svg)](https://badge.fury.io/py/aiida-zeopp)
        
        # aiida-zeopp
        
        AiiDA plugin for [Zeo++](http://www.zeoplusplus.org/)
        
        ## Installation
        
        ```shell
        pip install aiida-zeopp
        reentry scan
        verdi quicksetup  # better to set up a new profile
        verdi calculation plugins  # should now show your calclulation plugins
        ```
        
        ## Features
        
         * Add input structure in CIF format
          ```python
          CifData = DataFactory('cif')
          calc.use_structure(CifData(file='/path/to/file'))
          ```
         * Specify command line options using a python dictionary and `NetworkParameters`
          ```python
          d = { 'sa': [1.82, 1.82, 1000], 'volpo': [1.82, 1.82, 1000], 'chan': 1.2 }
          NetworkParameters = DataFactory('zeopp.parameters')
          inputs['parameters'] = NetworkParameters(dict=d)
          ```
         * `NetworkParameters` validates the command line options using [voluptuous](https://github.com/alecthomas/voluptuous).
           Find out about supported options:
          ```python
          NetworkParameters = DataFactory('zeopp.parameters')
          print(NetworkParameters.schema)
          ```
         * Add alternative atomic radii file
          ```python
          SinglefileData = DataFactory('singlefile')
          inputs['atomic_radii'] = SinglefileData(file='/path/to/file')
          ```
        
        ## Examples
        
        See `examples` folder for complete examples of setting up a calculation or workflow.
        
        ```shell
        verdi daemon start         # make sure the daemon is running
        cd examples
        verdi run submit.py        # runs test calculation
        ```
        
        ## Tests
        
        `aiida_zeopp` comes with a number of tests that are run at every commit.
        
        The following will discover and run all unit tests:
        ```shell
        pip install -e .[testing]
        pytest
        ```
        
        ## Analyzing output
        
        ```shell
        $ verdi process show 88
        -----------  ------------------------------------------------------------------------------
        type         NetworkCalculation
        pk           88
        uuid         deb63433-4dcd-4ca1-9165-cb97877496b3
        label        aiida_zeopp example calculation
        description  Converts .cif to .cssr format, computes surface area, pore volume and channels
        ctime        2018-11-19 09:12:55.259776+00:00
        mtime        2018-11-19 09:15:15.708275+00:00
        computer     [1] localhost
        code         network
        -----------  ------------------------------------------------------------------------------
        ##### INPUTS:
        Link label      PK  Type
        ------------  ----  -----------------
        parameters      87  NetworkParameters
        structure       86  CifData
        ##### OUTPUTS:
        Link label           PK  Type
        -----------------  ----  --------------
        remote_folder        89  RemoteData
        retrieved            90  FolderData
        structure_cssr       91  SinglefileData
        output_parameters    92  ParameterData
        
        $ verdi calcjob res 88
        {
          "ASA_A^2": 3532.09,
          "ASA_m^2/cm^3": 1932.13,
          "ASA_m^2/g": 2197.86,
          "Channel_surface_area_A^2": 3532.09,
          "Channels": {
            "Dimensionalities": [
              3
            ],
            "Largest_free_spheres": [
              6.74621
            ],
            "Largest_included_free_spheres": [
              13.1994
            ],
            "Largest_included_spheres": [
              13.1994
            ]
          },
          "Density": 0.879097,
          "Input_chan": 1.2,
          "Input_cssr": true,
          "Input_sa": [
            1.82,
            1.82,
            1000
          ],
          "Input_structure_filename": "HKUST-1.cif",
          "Input_volpo": [
            1.82,
            1.82,
            1000
          ],
          "NASA_A^2": 0.0,
          "NASA_m^2/cm^3": 0.0,
          "NASA_m^2/g": 0.0,
          "Number_of_channels": 1,
          "Number_of_pockets": 0,
          "POAV_A^3": 9049.01,
          "POAV_Volume_fraction": 0.495,
          "POAV_cm^3/g": 0.563078,
          "PONAV_A^3": 0.0,
          "PONAV_Volume_fraction": 0.0,
          "PONAV_cm^3/g": 0.0,
          "Pocket_surface_area_A^2": 0.0,
          "Unitcell_volume": 18280.8
        }
        
        $ verdi calcjob outputls 88
        _scheduler-stderr.txt
        _scheduler-stdout.txt
        out.chan
        out.cssr
        out.sa
        out.volpo
        
        $ verdi calcjob outputcat 88 -p out.sa
        @ out.sa Unitcell_volume: 18280.8   Density: 0.879097   ASA_A^2: 3532.09 ASA_m^2/cm^3: 1932.13 ASA_m^2/g: 2197.86 NASA_A^2: 0 NASA_m^2/cm^3: 0 NASA_m^2/g: 0
        Number_of_channels: 1 Channel_surface_area_A^2: 3532.09
        Number_of_pockets: 0 Pocket_surface_area_A^2:
        ```
        
        ## License
        
        MIT
        
        ## Contact
        leopold.talirz@gmail.com
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
Provides-Extra: testing
Provides-Extra: pre-commit
