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AiiDA plugin for zeo++

Project description

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# 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
verdi quicksetup # better to set up a new profile
verdi calculation plugins # should now show your calclulation plugins
```

## Usage

```shell
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
```

See `examples/submit.py` for an example of how to set up a calculation:

* Use `CifData` to specify input structure.
* (optional) Use `SinglefileData` to specify atomic radii file.
* Use `NetworkParameters` dictionary to specify other command line options.
For a complete list of supported command line options, see [here](aiida_zeopp/data/parameters.py)

## Tests

The following will discover and run all unit test:
```shell
pip install -e .[testing]
python manage.py
```

## Analyzing output

```shell
$ 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


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