Metadata-Version: 2.1
Name: aiida-zeopp
Version: 0.1.1
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: # aiida-zeopp
        
        AiiDA plugin for [Zeo++](http://www.zeoplusplus.org/)
        
        ## Installation
        
        ```shell
        git clone https://github.com/ltalirz/aiida-zeopp aiida-zeopp
        cd aiida-zeopp
        pip install -e .  # also installs aiida, if missing (but not postgres)
        reentry scan -r aiida  
        ```
        
        ## Tests
        
        ```shell
        python manage.py
        ```
        
        ## Usage
        A complete example of how to submit a test calculation using this plugin.
        
        ```shell
        $ verdi computer setup   # set up localhost for testing
        At any prompt, type ? to get some help.
        ---------------------------------------
        => Computer name: localhost
        Creating new computer with name 'localhost'
        => Fully-qualified hostname: localhost
        => Description: my local computer
        => Enabled: True
        => Transport type: local
        => Scheduler type: direct
        => AiiDA work directory: /tmp
        => mpirun command:
        => Default number of CPUs per machine: 4
        => Text to prepend to each command execution:
           # This is a multiline input, press CTRL+D on a
           # empty line when you finish
           # ------------------------------------------
           # End of old input. You can keep adding
           # lines, or press CTRL+D to store this value
           # ------------------------------------------
        => Text to append to each command execution:
           # This is a multiline input, press CTRL+D on a
           # empty line when you finish
           # ------------------------------------------
           # End of old input. You can keep adding
           # lines, or press CTRL+D to store this value
           # ------------------------------------------
        Computer 'localhost' successfully stored in DB.
        pk: 1, uuid: a5b452f0-ec1e-4ec2-956a-10a416f60ed3
        Note: before using it with AiiDA, configure it using the command
          verdi computer configure localhost
        (Note: machine_dependent transport parameters cannot be set via
        the command-line interface at the moment)
        
        $ verdi computer configure localhost
        Configuring computer 'localhost' for the AiiDA user 'leopold.talirz@epfl.ch'
        Computer localhost has transport of type local
        There are no special keys to be configured. Configuration completed.
        
        verdi code setup
        At any prompt, type ? to get some help.
        ---------------------------------------
        => Label: aiida_zeopp
        => Description: zeo++ 0.3
        => Local: False
        => Default input plugin: zeopp.network
        => Remote computer name: localhost
        => Remote absolute path: /Users/leopold/Personal/Postdoc-MARVEL/Projects/2017-09-15_pawel_plugin/zeo++-0.3/network
        => Text to prepend to each command execution
        FOR INSTANCE, MODULES TO BE LOADED FOR THIS CODE:
           # This is a multiline input, press CTRL+D on a
           # empty line when you finish
           # ------------------------------------------
           # End of old input. You can keep adding
           # lines, or press CTRL+D to store this value
           # ------------------------------------------
        => Text to append to each command execution:
           # This is a multiline input, press CTRL+D on a
           # empty line when you finish
           # ------------------------------------------
           # End of old input. You can keep adding
           # lines, or press CTRL+D to store this value
           # ------------------------------------------
        Code 'aiida_zeopp' successfully stored in DB.
        pk: 73, uuid: c89510a9-735f-4cd2-8421-bdf1da42f044
        
        $ verdi daemon start  # may need to 'verdi daemon configureuser'
        Clearing all locks ...
        Starting AiiDA Daemon ...
        Daemon started
        
        $ cd examples
        
        $ ./cli.py aiida_zeopp@localhost --submit
        submitted calculation; calc=Calculation(uuid='ac86b1a4-ccf1-489d-80ba-17c4e3304cb0') # ID=76
        
        $ verdi calculation list -a
        # Last daemon state_updater check: 0h:00m:28s ago (at 21:16:07 on 2018-01-09)
          PK  Creation    State             Sched. state    Computer    Type
        ----  ----------  ----------------  --------------  ----------  -------------
          76  19s ago     WITHSCHEDULER                     localhost   zeopp.network
        
        Total results: 1
        
        $ verdi calculation list -a
        # Last daemon state_updater check: 0h:00m:05s ago (at 21:23:37 on 2018-01-09)
          PK  Creation    State             Sched. state    Computer    Type
        ----  ----------  ----------------  --------------  ----------  -------------
          76  7m ago      FINISHED          DONE            localhost   zeopp.network
        
        Total results: 1
        
        $ verdi calculation show 76
        -----------  ------------------------------------
        type         NetworkCalculation
        pk           76
        uuid         ac86b1a4-ccf1-489d-80ba-17c4e3304cb0
        label        aiida_zeopp format conversion
        description  Test converting .cif to .cssr format
        ctime        2018-01-09 20:16:16.522201+00:00
        mtime        2018-01-09 20:16:41.107759+00:00
        computer     [1] localhost
        code         zeopp
        -----------  ------------------------------------
        ##### INPUTS:
        Link label         PK  Type
        ---------------  ----  -----------------
        input_structure    74  SinglefileData
        parameters         75  NetworkParameters
        ##### OUTPUTS:
        Link label       PK  Type
        -------------  ----  ----------
        remote_folder    77  RemoteData
        retrieved        78  FolderData
        structure_cssr   79  SinglefileData
        surface_area_sa  80  ParameterData
        channels_chan    81  SinglefileData
        pore_volume_volpo82  ParameterData
        
        $ verdi calculation outputls 76
        _scheduler-stderr.txt
        _scheduler-stdout.txt
        out.chan
        out.cssr
        out.sa
        out.volpo
        
        verdi calculation outputcat 76 -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:
        
        verdi calculation outputcat 76 -p out.sa
        
        $ verdi data parameter show 80
        {
          "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,
          "Density": 0.879097,
          "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,
          "Pocket_surface_area_A^2": 0.0,
          "Unitcell_volume": 18280.8
        }
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
Provides-Extra: pre-commit
Provides-Extra: testing
