{ "info": { "author": "Aliaksandr Yakutovich", "author_email": "aliaksandr.yakutovich@epfl.ch", "bugtrack_url": null, "classifiers": [ "Programming Language :: Python" ], "description": "[![PyPI version](https://badge.fury.io/py/aiida-raspa.svg)](https://badge.fury.io/py/aiida-raspa)\n\n# aiida-raspa\n\n[AiiDA](https://www.aiida.net) plugin for [RASPA2](https://github.com/numat/RASPA2).\n\n## Installation\n\nIf you use ``pip``, you can install it as:\n```\npip install aiida-raspa\n```\nIf you want to install the plugin in an editable mode, run:\n```\ngit clone https://github.com/yakutovicha/aiida-raspa\ncd aiida-raspa\npip install -e . # also installs aiida, if missing (but not postgres)\n```\nIn case the plugin does not appear in `verdi calculation plugins` list, run \n```\nreentry scan\n```\nand try again.\n\n\n## Examples\n\nSee `examples` folder for complete examples of setting up a calculation or workflow.\n\nsimple calculation:\n```shell\nverdi daemon restart # make sure the daemon is running\ncd examples/simple_calculations\nverdi run test_raspa_base.py --submit # submit test calculation\nverdi calculation list -a -p1 # check status of calculation\n```\nworkflow:\n```shell\nverdi daemon restart # make sure the daemon is running\ncd examples/workflows\nverdi run run_RaspaConverge_workflow.py # submit test calculation\nverdi work list -a -p1 # check status of calculation\n```\n\n## Analyzing output\n```shell\n$ verdi calculation show 7491\n----------- ------------------------------------\ntype RaspaCalculation\npk 7491\nuuid adc178d9-9f7e-4bbf-8283-8768f1964d9a\nlabel\ndescription\nctime 2019-01-10 15:38:20.103794+00:00\nmtime 2019-01-10 15:39:24.799300+00:00\ncomputer [3] deneb\ncode raspa\n----------- ------------------------------------\n##### INPUTS:\nLink label PK Type\n------------ ---- -------------\nparameters 7490 ParameterData\nstructure 7489 CifData\n##### OUTPUTS:\nLink label PK Type\n----------------- ---- -------------\nremote_folder 7492 RemoteData\nretrieved 7498 FolderData\noutput_parameters 7499 ParameterData\ncomponent_0 7500 ParameterData\n```\nResults that are for the framework and adsorbate can be obtained:\n```shell\n$ verdi calculation res 7491 # same as $ verdi data parameter show 7499\n{\n \"ads_ads_coulomb_energy_average\": 0.0, \n \"ads_ads_coulomb_energy_dev\": 0.0, \n \"ads_ads_coulomb_energy_unit\": \"kJ/mol\", \n \"ads_ads_total_energy_average\": -4.4408682910929, \n \"ads_ads_total_energy_dev\": 1.63152616602518, \n \"ads_ads_total_energy_unit\": \"kJ/mol\", \n \"ads_ads_vdw_energy_average\": -4.44086832435076, \n \"ads_ads_vdw_energy_dev\": 1.63152614939625, \n \"ads_ads_vdw_energy_unit\": \"kJ/mol\", \n \"adsorbate_density_average\": 26.35203, \n \"adsorbate_density_dev\": 4.63163, \n \"adsorbate_density_units\": \"kg/m^3\", \n \"cell_volume_average\": 12025.61229, \n \"cell_volume_dev\": 0.0, \n \"cell_volume_units\": \"A^3\", \n \"enthalpy_of_adsorption_average\": -2092.24759, \n \"enthalpy_of_adsorption_dev\": 315.039138, \n \"enthalpy_of_adsorption_units\": \"K\", \n \"exceeded_walltime\": false, \n \"framework_density\": \"739.995779685958\", \n \"framework_density_units\": \"kg/m^3\", \n \"framework_heat_capacity_average\": 3082.15209, \n \"framework_heat_capacity_dev\": 2889.16503, \n \"framework_heat_capacity_units\": \"J/mol/K\", \n \"host_ads_coulomb_energy_average\": 0.0, \n \"host_ads_coulomb_energy_dev\": 0.0, \n \"host_ads_coulomb_energy_unit\": \"kJ/mol\", \n \"host_ads_total_energy_average\": -176.211538447682, \n \"host_ads_total_energy_dev\": 36.0785945303337, \n \"host_ads_total_energy_unit\": \"kJ/mol\", \n \"host_ads_vdw_energy_average\": -176.211538455997, \n \"host_ads_vdw_energy_dev\": 36.0785944970758, \n \"host_ads_vdw_energy_unit\": \"kJ/mol\", \n \"pressure_average\": 0.0, \n \"pressure_dev\": 0.0, \n \"pressure_units\": \"Pa\", \n \"temperature_average\": 0.0, \n \"temperature_dev\": 0.0, \n \"temperature_units\": \"K\", \n \"total_energy_average\": -21727.4844, \n \"total_energy_dev\": 4526.71327, \n \"total_energy_units\": \"K\"\n}\n```\nComponent specific results can be obtained:\n```shell\n$ verdi data parameter show 7499\n{\n \"ads_ads_coulomb_energy_average\": 0.0, \n \"ads_ads_coulomb_energy_dev\": 0.0, \n \"ads_ads_coulomb_energy_unit\": \"kJ/mol\", \n \"ads_ads_total_energy_average\": -4.4408682910929, \n \"ads_ads_total_energy_dev\": 1.63152616602518, \n \"ads_ads_total_energy_unit\": \"kJ/mol\", \n \"ads_ads_vdw_energy_average\": -4.44086832435076, \n \"ads_ads_vdw_energy_dev\": 1.63152614939625, \n \"ads_ads_vdw_energy_unit\": \"kJ/mol\", \n \"adsorbate_density_average\": 26.35203, \n \"adsorbate_density_dev\": 4.63163, \n \"adsorbate_density_units\": \"kg/m^3\", \n \"cell_volume_average\": 12025.61229, \n \"cell_volume_dev\": 0.0, \n \"cell_volume_units\": \"A^3\", \n \"enthalpy_of_adsorption_average\": -2092.24759, \n \"enthalpy_of_adsorption_dev\": 315.039138, \n \"enthalpy_of_adsorption_units\": \"K\", \n \"exceeded_walltime\": false, \n \"framework_density\": \"739.995779685958\", \n \"framework_density_units\": \"kg/m^3\", \n \"framework_heat_capacity_average\": 3082.15209, \n \"framework_heat_capacity_dev\": 2889.16503, \n \"framework_heat_capacity_units\": \"J/mol/K\", \n \"host_ads_coulomb_energy_average\": 0.0, \n \"host_ads_coulomb_energy_dev\": 0.0, \n \"host_ads_coulomb_energy_unit\": \"kJ/mol\", \n \"host_ads_total_energy_average\": -176.211538447682, \n \"host_ads_total_energy_dev\": 36.0785945303337, \n \"host_ads_total_energy_unit\": \"kJ/mol\", \n \"host_ads_vdw_energy_average\": -176.211538455997, \n \"host_ads_vdw_energy_dev\": 36.0785944970758, \n \"host_ads_vdw_energy_unit\": \"kJ/mol\", \n \"pressure_average\": 0.0, \n \"pressure_dev\": 0.0, \n \"pressure_units\": \"Pa\", \n \"temperature_average\": 0.0, \n \"temperature_dev\": 0.0, \n \"temperature_units\": \"K\", \n \"total_energy_average\": -21727.4844, \n \"total_energy_dev\": 4526.71327, \n \"total_energy_units\": \"K\"\n}\n```\n\nFiles that are downloaded by the plugin to the local machine:\n```shell\n$ verdi calculation outputls 7491\n_scheduler-stderr.txt\n_scheduler-stdout.txt\noutput_framework_1.1.1_300.000000_500000.data\nrestart_framework_1.1.1_300.000000_500000\n```\n\nCat the output file:\n```shell\n$ verdi calculation outputcat 7491 -p output_framework_1.1.1_300.000000_500000.data\n...\nAverage adsorption energy _1-_0 obtained from Widom-insertion:\n(Note: the total heat of adsorption is dH=_1-_0 - - RT)\n=========================================================================\n\nSimulation finished, 1 warnings\nWARNING: INAPPROPRIATE NUMBER OF UNIT CELLS USED\n\n\nThu Jan 10 16:39:01 2019\nSimulation finished on Thursday, January 10.\nThe end time was 04:39 PM.\n```\n\n## License\n\nMIT\n\n## Contact\nyakutovicha@gmail.com\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", 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