Changelog

Until we get to a release version you may encounter different broken interface problem each time we increase a minor version.

Changes since v0.1.1

  • This should be the final release from this repository.

Changes since v0.1.0rc0

  • Rename SOAPify to cpctools

  • Clarify README

  • SOAPify.HDF5er.isTrajectoryGroup now returns False with Datasets

  • Added some simple cli interfaces

  • Added examples for LENS and tSOAP and for generating hdf5 files

  • Added getSOAPSettings() for getting the SOAP organization from a hdf5 dataset

  • Added getTimeSOAPSimple() to give the user a shortcut to solve memory problem with large SOAP datasets

  • Now createUniverseFromSlice() returns also types

  • added precision selection for storing the trajectories and the SOAP fingerprints

Changes since v0.0.6

  • The v0.0.6 has been set flagged as the ‘stable version’

  • Forced float64 precision in most of the calculations ← THIS IS A MAJOR CHANGE AND COULD IMPACT YOUR RESULTS

  • Changed the package name to cpctools, for storing it on https://pypi.org/

  • Removed the old and unused procedure for calculating the references

  • Compacted the workflows for a PR

  • Added the coveralls.io badge

  • Now documentation in rtd uses the standard rtd workflow

  • Refactored of the transition submodules, now support the ‘window’ and ‘stride’ concepts, added an entry to the documentation to explain it

  • Now saponifyMultipleTrajectories calls saponifyTrajectory

  • Moved HDF5er into SOAPify, to simplify the deployment

    • change your import HDF5er to import SOAPify.HDF5er as HDF5er in your old codes

    • HDF5er.HDF5erUtils → SOAPify.HDF5er.HDF5erUtils

    • HDF5er.HDF5To → SOAPify.HDF5er.HDF5To

    • HDF5er.ToHDF5 → SOAPify.HDF5er.ToHDF5

  • renamed some submodules to clarify the usage:

    • SOAPify.SOAPbase → SOAPify.distances

    • SOAPify.SOAPengine → SOAPify.engine

    • SOAPify.SOAPclassify → SOAPify.classify

    • SOAPify.SOAPTransitions → SOAPify.transitions

    • SOAPify.Saponify → SOAPify.saponify

  • renamed some functions to avoid naming collision, and to be more clear:

    • SOAPify.SOAPclassify.classify() → SOAPify.classify.applyClassification()

    • SOAPify.Saponify.saponifyGroup() → SOAPify.saponify.saponifyMultipleTrajectories()

    • SOAPify.Saponify.saponify() → SOAPify.saponify.saponifyTrajectory()

    • SOAPify.SOAPTransitions.normalizeMatrix() → SOAPify.transitions.normalizeMatrixByRow()

    • SOAPify.SOAPbase.KernelSoap() → SOAPify.distances.kernelSoap()

    • SOAPify.RemoveAtomIdentityFromEventTracker() → SOAPify.transitions.saponifyTrajectory()

  • Cleaned the code with pylint

  • Added LENS and tempoSOAP base functions

Changes since v0.0.4

  • Increased test coverage

  • Now if the box changes in a mda.Universe the ToHDF5 method saves it correctly

  • set quippy-ase compatibility to 0.9.10

  • Now tests prevents error in merging references

  • Checked and added python 3.10 compatibility

Changes since v0.0.3

  • getXYZfromTrajGroup now accept IO objects as inputs

  • WARNING: broken interface for getXYZfromTrajGroup, now it needs 3 inputs and the first is a file-like object

  • saveXYZfromTrajGroup and getXYZfromTrajGroup now can export comments per frames

  • transitionMatrixFromSOAPClassification now creates matrix with shape (n,n) and no more (n+1,n+1), where n is the lenght of the legend. The user will now need to address the errors in the legend, if needed

  • added calculateResidenceTimesFromClassification for calculating the residence times of the states during the MD

  • added trackStates for calculating the history of the evolution of the states in the MD

  • the result of trackStates can be used for calculating the residence times and the transition matrices

  • Now when appliyng soap, the created dataset will be given attributes that describe the parameters used for its creation

  • Removed some default values in function from Saponify and fillSOAPVectorFromdscribe

  • fillSOAPVectorFromdscribe now can fill soap vectors from multispecies calculations

  • changed slightly saponifyGroup and saponify: now they accept dscribe SOAP options as a dictionary, but not the sparse option

  • Now HDFTo.getXYZfromTrajGroup accepts slices as an option to export the trajectory

  • WARNING: broken interface for saponify

  • isTrajectoryGroup added to HDF5er to check if a group contain a trajectory in our format

  • now it is possible to select ‘quippy’ for calculating SOAP

  • tests reahul

  • fillSOAPVectorFromdscribe now is between 10 to 20 times faster than before

  • now name of the used engine is stored in the hdf5 file’s SOAP dataset

  • added a small utility to make the nmax/lmax/rcut getter work regardless the compatible dscribe engine

  • now installation procedure ignores dscribe/quippy: you should install them separately, but you do not need to wait for their compilation if you only need the analysis features

  • created getXYZfromMDA for exporting exyz files (with personalized header and columns) from mda universe

  • removed a bug in getXYZfromHDF5: now boxes are exported correctly

  • some QoL improvements behind the curtains and in the tests

  • added CI for documentation

  • merged src/HDF5er/MDA2HDF5.py and src/HDF5er/ase2HDF5.py into src/HDF5er/ToHDF5.py

  • Heavy changes in the documentation

  • Now the documentation coverage should work

  • Documentation now should also be hosted by readthedocs.io

Changes since v0.0.2a

  • Only for Monospecies systems: added a small utility (fillSOAPVectorFromdscribe) that returns the complete SOAP vector from the simplified one from dscribe

  • Added a utility for normalize SOAP vectors

  • Added createReferencesFromTrajectory that creates a variables that stores SOAP references

  • set up a way to classify with soap with a different method thant the original idea

  • the new references now can be loaded/unloaded on an hdf5 file

  • added a patch for hdf5 imported files: workaround for mda not loading correctly non orthogonal boxes from lammps dumps

Changes since v0.0.2

  • Added the possiblity to export xyz files from the hdf5 trajectories, also with extra data columns

  • Improved performance for getXYZfromTrajGroup

Changes since v0.0.1

  • Tests

  • Changed default imports for HDF5er

  • Adding override option to HDF5er.MDA2HDF5

  • Added 3rd neighbours in the References

  • Added attributes to HDF5er.MDA2HDF5

  • In the referenceMaker: added the possibility to choose lmax and nmax for SOAP

  • Added the possibility to export to hdf5 slices of the trajectories