Welcome to cpctools’s documentation!

cpctools

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We are no longer developing in this project. Future works will be in dynsight.

cpctools is a python 3.8/3.9/3.10 library aimed at simplifying the analysis of Molecular Dynamics simulations.

cpctools stands for Computational Physical Chemistry TOOLS, or, if you prefer, for Chemical Physics Computational TOOLS.

It contains two packages, SOAPify and SOAPify.HDF5er.

cpctools uses h5py to store the trajectories, the SOAP fingerprints, and the analysis results in a binary format, facilitated by HDF5er.

The documentation is available on read the docs. There you can consult the documentation for each available version of the package.

How To Install

To install the stable version of cpctools just type:

pip install cpctools

If you want to use dscribe or quippy for calculating the SOAP features you should install them separately, since they are quite heavy packages on their own, and usually you would use only one of these packages:

pip install "dscribe<=1.2.2,>1.2.0"
pip install "quippy-ase==0.9.10"

package: SOAPify

This package contains:

  • a toolbox to calculate the SOAP fingerprints of a system of atoms. The principal aim is to simplify the setup of the calculation. This toolbox depends on dscribe or quippy and ‘unify’ the output of the two codes.

  • a toolbox to calculate the distances between SOAP fingerprints

  • a simple analysis tool for trajectories of classified atoms

package: SOAPify.HDF5er

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

Our format is thought to speed up the calculations without occupying too much RAM, thanks to the hdf5 dataset chunking capabilities.

  • The data within the files are organized into Group categories:

    • “Trajectories” contains subgroups that represent the various stored trajectories, each trajectory subgroup contains three datasets:

      • “Types” contains the types of atoms in the simulation

      • “Box” contains the history of the box dimensions

      • “Trajectory” contains the history of the particle positions

    • “SOAP” group contains the Dastasets of the calculated SOAP fingerprints, each SOAP Dataset contains attributes with the settings to reproduce the results.

    • “Classification” contain a group per trajectory, the format of the Dataset contained within is not fixed

  • The user can choose to use a single file per project or to store separately the results of the various steps of the analysis project (this is more recommended). SOAPify.HDF5er contains a tool for exporting the trajectories from the hdf5 file to extended xyz format, compatible with ovito

Content

Packages

Indices and tables