| Name | aiida-zeopp JSON |
| Version |
2.0.0
JSON |
| download |
| home_page | None |
| Summary | AiiDA plugin for zeo++ |
| upload_time | 2023-08-26 23:59:27 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
aiida
workflows
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://github.com/lsmo-epfl/aiida-zeopp/actions)
[](https://badge.fury.io/py/aiida-zeopp)
[](https://github.com/ltalirz/aiida-zeopp/blob/master/LICENSE)
| Plugin | AiiDA | Python |
|-|-|-|
| `2.0.0` | ![Compatibility for v2.0][AiiDA v2.0] | [](https://pypi.org/project/aiida-zeopp) |
| `1.1.0` | ![Compatibility for v1.1][AiiDA v1.1] |  |
# aiida-zeopp
AiiDA plugin for [Zeo++](http://www.zeoplusplus.org/)
## Installation
```shell
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
```python
CifData = DataFactory('cif')
inputs['structure'] = CifData(file='/path/to/file')
```
* Specify command line options using a python dictionary and `NetworkParameters`
```python
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](https://github.com/alecthomas/voluptuous).
Find out about supported options:
```python
NetworkParameters = DataFactory('zeopp.parameters')
print(NetworkParameters.schema)
```
* Add alternative atomic radii file
```python
SinglefileData = DataFactory('singlefile')
inputs['atomic_radii'] = SinglefileData(file='/path/to/file')
```
## Examples
See `examples` folder for complete examples of setting up a calculation.
```shell
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:
```shell
pip install -e .[testing]
pytest
```
## Analyzing output
```shell
$ 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](<http://nccr-marvel.ch>) funded by the [Swiss National Science Foundation](<http://www.snf.ch/en>);
* the [swissuniversities P-5 project "Materials Cloud"](<https://www.materialscloud.org/swissuniversities>).
<img src="miscellaneous/logos/MARVEL.png" alt="MARVEL" style="padding:10px;" width="150"/>
<img src="miscellaneous/logos/swissuniversities.png" alt="swissuniversities" style="padding:10px;" width="250"/>
[AiiDA v1.1]: https://img.shields.io/badge/AiiDA->=1.4.4,<2.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D
[AiiDA v2.0]: https://img.shields.io/badge/AiiDA->=2.3.1,<3.0.0-007ec6.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACMAAAAhCAYAAABTERJSAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAAFhgAABYYBG6Yz4AAAABl0RVh0U29mdHdhcmUAd3d3Lmlua3NjYXBlLm9yZ5vuPBoAAAUbSURBVFiFzZhrbFRVEMd%2Fc%2B5uu6UUbIFC%2FUAUVEQCLbQJBIiBDyiImJiIhmohYNCkqJAQxASLF8tDgYRHBLXRhIcKNtFEhVDgAxBJqgmVh4JEKg3EIn2QYqBlt917xg%2BFss%2ByaDHOtzsz5z%2B%2FuZl7ztmF%2F5HJvxVQN6cPYX8%2FPLnOmsvNAvqfwuib%2FbNIk9cQeQnLcKRL5xLIV%2Fic9eJeunjPYbRs4FjQSpTB3aS1IpRKeeOOewajy%2FKKEO8Q0DuVdKy8IqsbPulxGHUfCBBu%2BwUYGuFuBTK7wQnht6PEbf4tlRomVRjCbXNjQEB0AyrFQOL5ENIJm7dTLZE6DPJCnEtFZVXDLny%2B4Sjv0PmmYu1ZdUek9RiMgoDmJ8V0L7XJqsZ3UW8YsBOwEeHeeFce7jEYXBy0m9m4BbXqSj2%2Bxnkg26MCVrN6DEZcwggtd8pTFx%2Fh3B9B50YLaFOPwXQKUt0tBLegtSomfBlfY13PwijbEnhztGzgJsK5h9W9qeWwBqjvyhB2iBs1Qz0AU974DciRGO8CVN8AJhAeMAdA3KbrKEtvxhsI%2B9emWiJlGBEU680Cfk%2BSsVqXZvcFYGXjF8ABVJ%2BTNfVXehyms1zzn1gmIOxLEB6E31%2FWBe5rnCarmo7elf7dJEeaLh80GasliI5F6Q9cAz1GY1OJVNDxTzQTw7iY%2FHEZRQY7xqJ9RU2LFe%2FYqakdP911ha0XhjjiTVAkDwgatWfCGeYocx8M3glG8g8EXhSrLrHnEFJ5Ymow%2FkhIYv6ttYUW1iFmEqqxdVoUs9FmsDYSqmtmJh3Cl1%2BVtl2s7owDUdocR5bceiyoSivGTT5vzpbzL1uoBpmcAAQgW7ArnKD9ng9rc%2BNgrobSNwpSkkhcRN%2BvmXLjIsDovYHHEfmsYFygPAnIDEQrQPzJYCOaLHLUfIt7Oq0LJn9fxkSgNCb1qEIQ5UKgT%2Fs6gJmVOOroJhQBXVqw118QtWLdyUxEP45sUpSzqP7RDdFYMyB9UReMiF1MzPwoUqHt8hjGFFeP5wZAbZ%2F0%2BcAtAAcji6LeSq%2FMYiAvSsdw3GtrfVSVFUBbIhwRWYR7yOcr%2FBi%2FB1MSJZ16JlgH1AGM3EO2QnmMyrSbTSiACgFBv4yCUapZkt9qwWVL7aeOyHvArJjm8%2Fz9BhdI4XcZgz2%2FvRALosjsk1ODOyMcJn9%2FYI6IrkS5vxMGdUwou2YKfyVqJpn5t9aNs3gbQMbdbkxnGdsr4bTHm2AxWo9yNZK4PXR3uzhAh%2BM0AZejnCrGdy0UvJxl0oMKgWSLR%2B1LH2aE9ViejiFs%2BXn6bTjng3MlIhJ1I1TkuLdg6OcAbD7Xx%2Bc3y9TrWAiSHqVkbZ2v9ilCo6s4AjwZCzFyD9mOL305nV9aonvsQeT2L0gVk4OwOJqXXVRW7naaxswDKVdlYLyMXAnntteYmws2xcVVZzq%2BtHPAooQggmJkc6TLSusOiL4RKgwzzYU1iFQgiUBA1H7E8yPau%2BZl9P7AblVNebtHqTgxLfRqrNvZWjsHZFuqMqKcDWdlFjF7UGvX8Jn24DyEAykJwNcdg0OvJ4p5pQ9tV6SMlP4A0PNh8aYze1ArROyUNTNouy8tNF3Rt0CSXb6bRFl4%2FIfQzNMjaE9WwpYOWQnOdEF%2BTdJNO0iFh7%2BI0kfORzQZb6P2kymS9oTxzBiM9rUqLWr1WE5G6ODhycQd%2FUnNVeMbcH68hYkGycNoUNWc8fxaxfwhDbHpfwM5oeTY7rUX8QAAAABJRU5ErkJggg%3D%3D
Raw data
{
"_id": null,
"home_page": null,
"name": "aiida-zeopp",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "aiida,workflows",
"author": null,
"author_email": "Leopold Talirz <leopold.talirz@epfl.ch>, Miriam Pougin <miriam.pougin@epfl.ch>",
"download_url": "https://files.pythonhosted.org/packages/b7/d6/f517d3b2ad078834753ba54ca10fbd75aa8d25b5c8f843d308b37648dd46/aiida_zeopp-2.0.0.tar.gz",
"platform": null,
"description": "[](https://github.com/lsmo-epfl/aiida-zeopp/actions)\n[](https://badge.fury.io/py/aiida-zeopp)\n[](https://github.com/ltalirz/aiida-zeopp/blob/master/LICENSE)\n\n| Plugin | AiiDA | Python |\n|-|-|-|\n| `2.0.0` | ![Compatibility for v2.0][AiiDA v2.0] | [](https://pypi.org/project/aiida-zeopp) |\n| `1.1.0` | ![Compatibility for v1.1][AiiDA v1.1] |  |\n\n\n# aiida-zeopp\n\nAiiDA plugin for [Zeo++](http://www.zeoplusplus.org/)\n\n## Installation\n\n```shell\npip install aiida-zeopp\nreentry scan\nverdi quicksetup # better to set up a new profile\nverdi calculation plugins # should now show your calclulation plugins\n```\n\n## Features\n\n * Add input structure in CIF format\n ```python\n CifData = DataFactory('cif')\n inputs['structure'] = CifData(file='/path/to/file')\n ```\n * Specify command line options using a python dictionary and `NetworkParameters`\n ```python\n d = { 'sa': [1.82, 1.82, 1000], 'volpo': [1.82, 1.82, 1000], 'chan': 1.2 }\n NetworkParameters = DataFactory('zeopp.parameters')\n inputs['parameters'] = NetworkParameters(dict=d)\n ```\n * `NetworkParameters` validates the command line options using [voluptuous](https://github.com/alecthomas/voluptuous).\n Find out about supported options:\n ```python\n NetworkParameters = DataFactory('zeopp.parameters')\n print(NetworkParameters.schema)\n ```\n * Add alternative atomic radii file\n ```python\n SinglefileData = DataFactory('singlefile')\n inputs['atomic_radii'] = SinglefileData(file='/path/to/file')\n ```\n\n## Examples\n\nSee `examples` folder for complete examples of setting up a calculation.\n\n```shell\nverdi daemon start # make sure the daemon is running\ncd examples\nverdi run examples/example_01.py # runs test calculatio\n```\n\n## Tests\n\n`aiida_zeopp` comes with a number of tests that are run at every commit.\n\nThe following will discover and run all unit tests:\n```shell\npip install -e .[testing]\npytest\n```\n\n## Analyzing output\n\n```shell\n$ verdi process show 88\n----------- ------------------------------------------------------------------------------\ntype NetworkCalculation\npk 88\nuuid deb63433-4dcd-4ca1-9165-cb97877496b3\nlabel aiida_zeopp example calculation\ndescription Converts .cif to .cssr format, computes surface area, pore volume and channels\nctime 2018-11-19 09:12:55.259776+00:00\nmtime 2018-11-19 09:15:15.708275+00:00\ncomputer [1] localhost\ncode network\n----------- ------------------------------------------------------------------------------\n##### INPUTS:\nLink label PK Type\n------------ ---- -----------------\nparameters 87 NetworkParameters\nstructure 86 CifData\n##### OUTPUTS:\nLink label PK Type\n----------------- ---- --------------\nremote_folder 89 RemoteData\nretrieved 90 FolderData\nstructure_cssr 91 SinglefileData\noutput_parameters 92 ParameterData\n\n$ verdi calcjob res 88\n{\n \"ASA_A^2\": 3532.09,\n \"ASA_m^2/cm^3\": 1932.13,\n \"ASA_m^2/g\": 2197.86,\n \"Channel_surface_area_A^2\": 3532.09,\n \"Channels\": {\n \"Dimensionalities\": [\n 3\n ],\n \"Largest_free_spheres\": [\n 6.74621\n ],\n \"Largest_included_free_spheres\": [\n 13.1994\n ],\n \"Largest_included_spheres\": [\n 13.1994\n ]\n },\n \"Density\": 0.879097,\n \"Input_chan\": 1.2,\n \"Input_cssr\": true,\n \"Input_sa\": [\n 1.82,\n 1.82,\n 1000\n ],\n \"Input_structure_filename\": \"HKUST-1.cif\",\n \"Input_volpo\": [\n 1.82,\n 1.82,\n 1000\n ],\n \"NASA_A^2\": 0.0,\n \"NASA_m^2/cm^3\": 0.0,\n \"NASA_m^2/g\": 0.0,\n \"Number_of_channels\": 1,\n \"Number_of_pockets\": 0,\n \"POAV_A^3\": 9049.01,\n \"POAV_Volume_fraction\": 0.495,\n \"POAV_cm^3/g\": 0.563078,\n \"PONAV_A^3\": 0.0,\n \"PONAV_Volume_fraction\": 0.0,\n \"PONAV_cm^3/g\": 0.0,\n \"Pocket_surface_area_A^2\": 0.0,\n \"Unitcell_volume\": 18280.8\n}\n\n$ verdi calcjob outputls 88\n_scheduler-stderr.txt\n_scheduler-stdout.txt\nout.chan\nout.cssr\nout.sa\nout.volpo\n\n$ verdi calcjob outputcat 88 -p out.sa\n@ 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\nNumber_of_channels: 1 Channel_surface_area_A^2: 3532.09\nNumber_of_pockets: 0 Pocket_surface_area_A^2:\n```\n\n## License\n\nMIT\n\n## Contact\nleopold.talirz@gmail.com\n\n\n## Acknowledgements\nThis work is supported by:\n* the [MARVEL National Centre for Competency in Research](<http://nccr-marvel.ch>) funded by the [Swiss National Science Foundation](<http://www.snf.ch/en>);\n* the [swissuniversities P-5 project \"Materials Cloud\"](<https://www.materialscloud.org/swissuniversities>).\n\n<img src=\"miscellaneous/logos/MARVEL.png\" alt=\"MARVEL\" style=\"padding:10px;\" width=\"150\"/>\n<img src=\"miscellaneous/logos/swissuniversities.png\" alt=\"swissuniversities\" style=\"padding:10px;\" width=\"250\"/>\n\n[AiiDA v1.1]: 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v2.0]: 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