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https://github.com/TRI-AMDD/piro

Software for evaluating pareto-optimal synthesis pathways
https://github.com/TRI-AMDD/piro

Last synced: 2 months ago
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Software for evaluating pareto-optimal synthesis pathways

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README 

        
# *piro:* rational planning of solid-state synthesis routes for inorganics

![Testing - main](https://github.com/TRI-AMDD/piro/workflows/Testing%20-%20main/badge.svg)

![Linting](https://github.com/TRI-AMDD/piro/workflows/Linting/badge.svg)

[![Coverage Status](https://coveralls.io/repos/github/TRI-AMDD/piro/badge.svg?branch=test)](https://coveralls.io/github/TRI-AMDD/piro?branch=test)



_piro_ is a recommendation system for navigation and planning of synthesis of

inorganic materials based on classical nucleation theory

and semi-empirical, data-driven approximations to its parts. Currently it

works with Materials Project data via its Rester API.



- _piro_ creates synthesis reaction planning plots for target polymorphs under a specific set of thermodynamic conditions and a precursor library, 

where favorable routes are those that are (nearly) Pareto optimal in terms of two metrics: nucleation barrier and phase-selection.



- _piro_ allows retrosynthetic analysis of target inorganic materials to generate a synthesis reaction tree.

(i.e. laying out the reaction pathways necessary to arrive at the target from practical/purchasable reagents/starting materials)



- _piro_ supports generation of interactive plots and a web-UI for easy-navigation.



Tutorial jupyter notebooks showing how to use _piro_ locally are provided in the [notebooks](piro/notebooks) folder.



## Prerequisites



### Python 3.9

 - `piro` uses Python 3.9.  If you wish to develop or run a local server, you can also following the Docker instructions below to create your own `piro` container instead of configuring your local environment.



### Pymatgen API key

 - `piro` has a dependency on `pymatgen` which requires you to generate an API key.  Go [here](https://materialsproject.org/open) and follow the instructions to generate your API key.

 - Use the API key by either

    - A) adding the environment variable MAPI_KEY to your current environment

    ```

    # for example in the terminal

    export MAPI_KEY=

    ```  

    - B) using pymatgen's command line to set a global key (note: it's PMG_MAPI_KEY instead of just MAPI_KEY)

    ```

    pmg config --add PMG_MAPI_KEY 

    ```



### Access to MongoDB Cached Database (optional)

 - Once you get the credential, set up the environment variable as follow:

      ```

      MONGODB_URI = mongodb://{username}:{password}@{host}:{port}/{database}

      ```

 - If you use conda for your development, you can do like this:

      ```

      conda env config vars set MONGODB_URI="mongodb://{username}:{password}@{host}:{port}/{database}"

      ```

 - You will need to reactive the conda environment so the change will take effective.



## Setup

There are a few options to install and run `piro` on your machine:



###  A) Get `piro` from PyPI

The most recent stable version of `piro` can be installed from [PyPI](https://pypi.org/project/piro/). We recommend installing `piro` in a dedicated environment to avoid any version conflicts for its dependencies.

```

pip install piro

```



###  B) For development, install the source from this repo in development mode

```

python setup.py develop

```



## Piro Module Usage

 - Try out a Jupyter notebook:

    ```

    jupyter notebook

    ```

   See the notebooks in piro/notebooks



## Web app



[README](web/README.md)



## Citation

If you use `piro`, we kindly ask you to cite the following publication:

* Aykol, M., Montoya, J.H., Hummelshøj, J. "Rational Solid-State Synthesis Routes for Inorganic Materials" J. Am. Chem. Soc. (2021): [https://doi.org/10.1021/jacs.1c04888](https://doi.org/10.1021/jacs.1c04888)