SOAPify, HDF5er and ReferenceMaker

To setup the environment just run in the repository folder:

python3 -m venv ./venv --prompt SOAPenv
source ./venv/bin/activate
pip install --upgrade pip wheel
pip install -r requirements

and then you can install the package with:

pip install .

SOAPify

This package contains a toolbox to calculate the SOAP fingerprints of a system of atoms.

HDF5er

This package contains a small toolbox to create hdf5 files with h5py from trajectory and topology files. The format we use do not align with h5md.

ReferenceMaker

The ReferenceMaker package contains a set of function that can create a reference file to be used with the SOAPify package.

ReferenceMaker function can be called with custom made scripts, but the user can create a list of SOAP references with the following:

python3 -m ReferenceMaker

The command will create a file called “XxReferences.hdf5” (with Xx is the chemical symbol of the chosen metal in the prompt from the command python3 -m ReferenceMaker) that contains the fingerprints of the following structures:

bulk: sc,bcc,hcp,fcc
th4116: vertexes, edges, 001 faces, 111 faces
ico5083: vertexes, edges, 111 faces, five folded axis
dh3049: concave atom, five folded axis

To use the automatic procedure the user needs to install lammps as a python package so that lammps is avaiable to the newly created virtual environment, following the guide on the lammps site