AiiDA plugin for zeo++
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README.md

Build Status Coverage Status Docs status PyPI version

aiida-zeopp

AiiDA plugin for Zeo++

Installation

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
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
CifData = DataFactory('cif')
calc.use_structure(CifData(file='/path/to/file'))
  • Specify command line options using a python dictionary and NetworkParameters
d = { 'sa': [1.82, 1.82, 1000], 'volpo': [1.82, 1.82, 1000], 'chan': 1.2 }
NetworkParameters = DataFactory('zeopp.parameters')
calc.use_parameters(NetworkParameters(dict=d))
  • NetworkParameters validates the command line options using voluptuous. Find out about supported options:
NetworkParameters = DataFactory('zeopp.parameters')
print(NetworkParameters.schema)
  • Add alternative atomic radii file
SinglefileData = DataFactory('singlefile')
calc.use_atomic_radii(SinglefileData(file='/path/to/file'))

Examples

See examples folder for complete examples of setting up a calculation or workflow.

verdi daemon start         # make sure the daemon is running
cd examples
verdi run submit.py        # submit test calculation
verdi calculation list -a  # check status of 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:

pip install -e .[testing]
python manage.py

Analyzing output

$ verdi calculation 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 calculation 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 calculation outputls 88
_scheduler-stderr.txt
_scheduler-stdout.txt
out.chan
out.cssr
out.sa
out.volpo

$ verdi calculation 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