Description:
aiidazeopp 2.0.0
Plugin
AiiDA
Python
2.0.0
1.1.0
aiida-zeopp
AiiDA plugin for Zeo++
Installation
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
CifData = DataFactory('cif')
inputs['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')
inputs['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')
inputs['atomic_radii'] = SinglefileData(file='/path/to/file')
Examples
See examples folder for complete examples of setting up a calculation.
verdi daemon start # make sure the daemon is running
cd examples
verdi run examples/example_01.py # runs test calculatio
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]
pytest
Analyzing output
$ 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
Acknowledgements
This work is supported by:
the MARVEL National Centre for Competency in Research funded by the Swiss National Science Foundation;
the swissuniversities P-5 project "Materials Cloud".
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Customer Reviews
There are no reviews.
