Installing

Installing via Conda

In progress

Installing via pip

In progress

Installing from source

pyEELSMODEL can be installed by cloning the repository to your computer via:

$ git clone https://github.com/joverbee/pyEELSMODEL.git

The next step is to navigate to the pyEELMODEL directory and type following into the command line:

$ pip3 install .

If you want to create an editable install one needs to do following:

$ pip3 install -e .

In the future, the package will be published on PyPI simplifying the installation procedure.

Setting up GOS tables

After installation, the generalized oscillator strengths (GOS) tables should be imported. The GOS tables are necessary to perform EEL quantification since they are used to calculate the atomic cross sections. Two different GOS tables can be used for quantification:

  1. The GOS tables calculated by Zhang Z. et al. which can be found at doi:10.5281/zenodo.7729585.

  2. The GOS tables calculated by Segger L. et al. which can be found at doi:10.5281/zenodo.7645765.

To know where your pyEELSMODEL package is installed following command can be run in a python console:

import pyEELSMODEL
print(pyEELSMODEL.__path__)

This information is necessary for the proper use of the GOS tables.

GOS tables from Zhang Z.

Following steps explain on how the properly setup the GOS array of Zhang Z.

  1. Download the Dirac_GOS_database.zip file

  2. Unzip the file

  3. Copy the .hdf5 files in the folder to the .pyEELSMODEL\database\Zhang folder which is found in the pyEELSMODEL folder

The GOS tables from Zhang Z. are used as default in the quantification workflows.

GOS tables from Segger L.

Following steps explain on how the properly setup the GOS array of Segger L:

  1. Download the Segger_Guzzinati_Kohl_1.5.0.gosh (depends on version) file

  2. Copy the .gosh file to .pyEELMODEL\database\Segger_Guzzinati_Kohl folder which is found in the pyEELSMODEL folder

Both cross sections are used in the notebook examples hence both need to be incorporated