Installation

The code supports Python 3.8 and newer.

Clone repository

$ git clone https://github.com/paolodeangelis/SEI_builder.git

Set up Python enviroment

To set up your environment, we show the steps using both pip (PyPI) or conda (Anaconda) package-management.

  1. move in the SEI Builder folder

    $ cd SEI_builder

  2. create a virtual environment venv_sei

    1. create the enviroment with venv

    $ python3 -m venv venv_sei

    1. activate it

    $ source venv_sei/bin/activate

    Note

    Once activate the python environment at the begging of the command line, you have (venv_sei). To exit from the virtual environment, execute the command deactivate.

    1. install depedecy

    (venv_sei)$ pip install -r requirements.txt

    Warning

    check if all the jupyter widget are working:

    $ jupyter labextension list
JupyterLab v3.1.17
/.../venv_sei/share/jupyter/labextensions
       nglview-js-widgets v3.0.1 enabled OK
       jupyterlab-plotly v5.3.1 enabled OK
       @jupyter-widgets/jupyterlab-manager v3.0.1 enabled OK (python, jupyterlab_widgets)
       @bokeh/jupyter_bokeh v3.0.4 enabled OK (python, jupyter_bokeh)

    if the line nglview-js-widgets v3.0.1 enabled OK is missing, run the following command:

    $ pip install --force-reinstall nglview

Install packmol

Inside the code we use the code Packmol by Martínez et al.[1]

  1. Clone from repository

    $ git clone https://github.com/m3g/packmol.git

  2. Compile it

    $ cd packmol
$ make

    Warning

    If make raises an error usually means that a compiler is missing. For example:

    $ make
make: /usr/bin/gfortran: Command not found
make: *** [Makefile:116: sizes.o] Error 127

    The solution is to install the missing compiler with the following commands

    $ sudo apt update
$ sudo apt install build-essential

  1. (optional) create a symbolic link to local bin folder

    $ ln -s $(pwd)/packmol /home/$USER/.local/bin/packmol

Configure the Material Project API key

  1. Get Material Project API key

    Access to Material Project and follow the instructions on the documentation.

  2. Make the configuration file

    Run the script mpinterfaces_setup.py replacing <MATERIAL_PROJECT_KEY> with the API key got in the previus step.

    $ python3 mpinterfaces_setup.py -k <MATERIAL_PROJECT_KEY>