Welcome to SOAPify’s documentation!
SOAPify, HDF5er and ReferenceMaker
SOAPify is python 3.8/3.9/3.10 library aimed at simplify the analysis of Molecular Dynamics simulation using the Smooth Overlap of Atomic Position (SOAP) in context that includes the time along the geometrical informations of the frames of the simulation.
SOAPify uses h5py for caching the results of the various analysis.
SOAPify offers a suite for a (basic) state analysis for the simulation.
How To Install
To set up the environment and install SOAPify run the following in the repository folder:
python3 -m venv ./venv --prompt SOAPify
source ./venv/bin/activate
pip install --upgrade pip
pip install .
If you want to use dscribe or quippy for calculating the SOAP features you should install them separately:
pip install "dscribe >1.2.0 <=1.2.2"
pip install "quippy-ase==0.9.10"
(PyPI support is incoming!)
Now with a (very basic) documentation of the latest version pushed to the main branch!
A more complete history of the documetation is avaiable on read the docs, with storage of the old
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
Modules
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SOAPify HDF5er ReferenceMaker