Metadata-Version: 2.4
Name: aiidalab-qe-pp
Version: 0.1.3
Summary: AiiDAlab quantum ESPRESSO app plugin for PP code
Author: Andres Ortega-Guerrero
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: AiiDA
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3
License-File: LICENSE
Requires-Dist: weas-widget==0.1.25
Requires-Dist: aiida-pythonjob==0.1.8
Requires-Dist: scikit-image
Requires-Dist: kaleido
Requires-Dist: ruff ; extra == "dev"
Project-URL: Homepage, https://github.com/AndresOrtegaGuerrero/aiidalab-qe-pp
Provides-Extra: dev

# aiidalab-qe-pp
Plugin to perform data analysis and plotting using the pp.x code for the  [AiiDAlab Quantum ESPRESSO application](https://github.com/aiidalab/aiidalab-qe)

## Installation
To install the `aiidalab-qe-pp` plugin, follow these steps:

```shell
git clone https://github.com/AndresOrtegaGuerrero/aiidalab-qe-pp.git
cd aiidalab-qe-pp
pip install -e .
```

## Python

This plugin enables the computation of reduced-size cube files generated from Python using the [AiiDA-PythonJob plugin](https://github.com/aiidateam/aiida-pythonjob).
To ensure compatibility, set up an AiiDA code that utilizes the same Python version as your AiiDAlab environment.
Ensure that your environment includes the `pymatgen` , `cloudpickle` and `scikit-image` libraries.
Once configured, you can set up your AiiDA code with the following command:


```bash
verdi code create core.code.installed --config python_code.yml
```

In the `python_code.yml` file, specify the configuration for your HPC system within AiiDAlab as follows:

```bash
---
label: 'python-py39'
description: 'python at daint alps'
default_calc_job_plugin: 'pythonjob.pythonjob'
filepath_executable: '/users/username/miniconda3/envs/py39/bin/python'
computer: 'daint-alps'
prepend_text: |
   conda activate py39

append_text: ' '
```


## Critic2 Integration

This plugin utilizes [Critic2](https://aoterodelaroza.github.io/critic2/) software to compute Scanning Tunneling Microscopy (STM) images from Quantum ESPRESSO output data.
For more information on Critic2 and its capabilities, please visit the [official Critic2 website](https://aoterodelaroza.github.io/critic2/).

## Critic2 AiiDAlab Installation

For installing Critic2 in your AiiDAlab please ensure you have gfortran and cmake

```shell
mamba install gfortran
mamba install cmake
```

Then follow the instructions for [Critic2 Installation](https://aoterodelaroza.github.io/critic2/installation/)

Onced installed critic2

```bash
verdi code create core.code.installed --config code.yml
```
where code.yml for your localhost within AiiDAlab can be

```bash
---
label: 'critic2'
description: 'Critic 2 at localhost'
default_calc_job_plugin: 'critic2'
filepath_executable: '/home/jovyan/critic2/build/src/critic2'
computer: 'localhost'
prepend_text: |

append_text: ' '
```

## License
The `aiidalab-qe-pp` plugin package is released under the MIT license.
See the `LICENSE` file for more details.

## Contact

If you have any questions or suggestions, feel free to reach out:

- **Author**: Andres Ortega-Guerrero
- **Email**: [andres.ortega-guerrero@empa.ch](andres.ortega-guerrero@empa.ch)

## Acknowledgements
We acknowledge support from:
* the [NCCR MARVEL](http://nccr-marvel.ch/) funded by the Swiss National Science Foundation;

