Metadata-Version: 2.1
Name: aiida-raspa
Version: 1.0.0a1
Summary: AiiDA plugin for RASPA code
Home-page: https://github.com/yakutovicha/aiida-raspa
Author: Aliaksandr Yakutovich
Author-email: aliaksandr.yakutovich@epfl.ch
License: MIT License
Description: [![PyPI version](https://badge.fury.io/py/aiida-raspa.svg)](https://badge.fury.io/py/aiida-raspa)
        
        # aiida-raspa
        
        [AiiDA](http://www.aiida.net/) plugin for [RASPA2](https://github.com/iRASPA/RASPA2).
        
        ## Installation
        
        If you use ``pip``, you can install it as:
        ```
        pip install aiida-raspa
        ```
        If you want to install the plugin in an editable mode, run:
        ```
        git clone https://github.com/yakutovicha/aiida-raspa
        cd aiida-raspa
        pip install -e .  # also installs aiida, if missing (but not postgres)
        ```
        In case the plugin does not appear in `verdi calculation plugins` list, run 
        ```
        reentry scan
        ```
        and try again.
        
        
        ## Examples
        
        See `examples` folder for complete examples of setting up a calculation or workflow.
        
        simple calculation:
        ```shell
        verdi daemon restart                                   # make sure the daemon is running
        cd examples/simple_calculations
        verdi run test_raspa_base.py <code_label> --submit     # submit test calculation
        verdi calculation list -a -p1                          # check status of calculation
        ```
        workflow:
        ```shell
        verdi daemon restart                                   # make sure the daemon is running
        cd examples/workflows
        verdi run run_RaspaConverge_workflow.py  <code_label>  # submit test calculation
        verdi work list -a -p1                                 # check status of calculation
        ```
        
        ## Analyzing output
        ```shell
        $ verdi calculation show 7491
        -----------  ------------------------------------
        type         RaspaCalculation
        pk           7491
        uuid         adc178d9-9f7e-4bbf-8283-8768f1964d9a
        label
        description
        ctime        2019-01-10 15:38:20.103794+00:00
        mtime        2019-01-10 15:39:24.799300+00:00
        computer     [3] deneb
        code         raspa
        -----------  ------------------------------------
        ##### INPUTS:
        Link label      PK  Type
        ------------  ----  -------------
        parameters    7490  ParameterData
        structure     7489  CifData
        ##### OUTPUTS:
        Link label           PK  Type
        -----------------  ----  -------------
        remote_folder      7492  RemoteData
        retrieved          7498  FolderData
        output_parameters  7499  ParameterData
        component_0        7500  ParameterData
        ```
        Results that are for the framework and adsorbate can be obtained:
        ```shell
        $ verdi calculation res 7491 # same as $ verdi data parameter show 7499
        {
          "ads_ads_coulomb_energy_average": 0.0, 
          "ads_ads_coulomb_energy_dev": 0.0, 
          "ads_ads_coulomb_energy_unit": "kJ/mol", 
          "ads_ads_total_energy_average": -4.4408682910929, 
          "ads_ads_total_energy_dev": 1.63152616602518, 
          "ads_ads_total_energy_unit": "kJ/mol", 
          "ads_ads_vdw_energy_average": -4.44086832435076, 
          "ads_ads_vdw_energy_dev": 1.63152614939625, 
          "ads_ads_vdw_energy_unit": "kJ/mol", 
          "adsorbate_density_average": 26.35203, 
          "adsorbate_density_dev": 4.63163, 
          "adsorbate_density_units": "kg/m^3", 
          "cell_volume_average": 12025.61229, 
          "cell_volume_dev": 0.0, 
          "cell_volume_units": "A^3", 
          "enthalpy_of_adsorption_average": -2092.24759, 
          "enthalpy_of_adsorption_dev": 315.039138, 
          "enthalpy_of_adsorption_units": "K", 
          "exceeded_walltime": false, 
          "framework_density": "739.995779685958", 
          "framework_density_units": "kg/m^3", 
          "framework_heat_capacity_average": 3082.15209, 
          "framework_heat_capacity_dev": 2889.16503, 
          "framework_heat_capacity_units": "J/mol/K", 
          "host_ads_coulomb_energy_average": 0.0, 
          "host_ads_coulomb_energy_dev": 0.0, 
          "host_ads_coulomb_energy_unit": "kJ/mol", 
          "host_ads_total_energy_average": -176.211538447682, 
          "host_ads_total_energy_dev": 36.0785945303337, 
          "host_ads_total_energy_unit": "kJ/mol", 
          "host_ads_vdw_energy_average": -176.211538455997, 
          "host_ads_vdw_energy_dev": 36.0785944970758, 
          "host_ads_vdw_energy_unit": "kJ/mol", 
          "pressure_average": 0.0, 
          "pressure_dev": 0.0, 
          "pressure_units": "Pa", 
          "temperature_average": 0.0, 
          "temperature_dev": 0.0, 
          "temperature_units": "K", 
          "total_energy_average": -21727.4844, 
          "total_energy_dev": 4526.71327, 
          "total_energy_units": "K"
        }
        ```
        Component specific results can be obtained:
        ```shell
        $ verdi data parameter show 7499
        {
          "ads_ads_coulomb_energy_average": 0.0, 
          "ads_ads_coulomb_energy_dev": 0.0, 
          "ads_ads_coulomb_energy_unit": "kJ/mol", 
          "ads_ads_total_energy_average": -4.4408682910929, 
          "ads_ads_total_energy_dev": 1.63152616602518, 
          "ads_ads_total_energy_unit": "kJ/mol", 
          "ads_ads_vdw_energy_average": -4.44086832435076, 
          "ads_ads_vdw_energy_dev": 1.63152614939625, 
          "ads_ads_vdw_energy_unit": "kJ/mol", 
          "adsorbate_density_average": 26.35203, 
          "adsorbate_density_dev": 4.63163, 
          "adsorbate_density_units": "kg/m^3", 
          "cell_volume_average": 12025.61229, 
          "cell_volume_dev": 0.0, 
          "cell_volume_units": "A^3", 
          "enthalpy_of_adsorption_average": -2092.24759, 
          "enthalpy_of_adsorption_dev": 315.039138, 
          "enthalpy_of_adsorption_units": "K", 
          "exceeded_walltime": false, 
          "framework_density": "739.995779685958", 
          "framework_density_units": "kg/m^3", 
          "framework_heat_capacity_average": 3082.15209, 
          "framework_heat_capacity_dev": 2889.16503, 
          "framework_heat_capacity_units": "J/mol/K", 
          "host_ads_coulomb_energy_average": 0.0, 
          "host_ads_coulomb_energy_dev": 0.0, 
          "host_ads_coulomb_energy_unit": "kJ/mol", 
          "host_ads_total_energy_average": -176.211538447682, 
          "host_ads_total_energy_dev": 36.0785945303337, 
          "host_ads_total_energy_unit": "kJ/mol", 
          "host_ads_vdw_energy_average": -176.211538455997, 
          "host_ads_vdw_energy_dev": 36.0785944970758, 
          "host_ads_vdw_energy_unit": "kJ/mol", 
          "pressure_average": 0.0, 
          "pressure_dev": 0.0, 
          "pressure_units": "Pa", 
          "temperature_average": 0.0, 
          "temperature_dev": 0.0, 
          "temperature_units": "K", 
          "total_energy_average": -21727.4844, 
          "total_energy_dev": 4526.71327, 
          "total_energy_units": "K"
        }
        ```
        
        Files that are downloaded by the plugin to the local machine:
        ```shell
        $ verdi calculation outputls 7491
        _scheduler-stderr.txt
        _scheduler-stdout.txt
        output_framework_1.1.1_300.000000_500000.data
        restart_framework_1.1.1_300.000000_500000
        ```
        
        Cat the output file:
        ```shell
        $ verdi calculation outputcat 7491 -p output_framework_1.1.1_300.000000_500000.data
        ...
        Average adsorption energy <U_gh>_1-<U_h>_0 obtained from Widom-insertion:
        (Note: the total heat of adsorption is dH=<U_gh>_1-<U_h>_0 - <U_g> - RT)
        =========================================================================
        
        Simulation finished,  1 warnings
        WARNING: INAPPROPRIATE NUMBER OF UNIT CELLS USED
        
        
        Thu Jan 10 16:39:01 2019
        Simulation finished on Thursday, January 10.
        The end time was 04:39 PM.
        ```
        
        ## License
        
        MIT
        
        ## Contact
        yakutovicha@gmail.com
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Development Status :: 4 - Beta
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: pre-commit
