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 returnsFalse
with DatasetsAdded 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 datasetAdded
getTimeSOAPSimple()
to give the user a shortcut to solve memory problem with large SOAP datasetsNow
createUniverseFromSlice()
returns also typesadded 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
callssaponifyTrajectory
Moved HDF5er into SOAPify, to simplify the deployment
change your
import HDF5er
toimport SOAPify.HDF5er as HDF5er
in your old codesHDF5er.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 inputsWARNING: broken interface for
getXYZfromTrajGroup
, now it needs 3 inputs and the first is a file-like objectsaveXYZfromTrajGroup
andgetXYZfromTrajGroup
now can export comments per framestransitionMatrixFromSOAPClassification
now creates matrix with shape(n,n)
and no more(n+1,n+1)
, wheren
is the lenght of the legend. The user will now need to address the errors in the legend, if neededadded
calculateResidenceTimesFromClassification
for calculating the residence times of the states during the MDadded
trackStates
for calculating the history of the evolution of the states in the MDthe result of
trackStates
can be used for calculating the residence times and the transition matricesNow 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
andsaponify
: now they accept dscribe SOAP options as a dictionary, but not the sparse optionNow 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 formatnow 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 universeremoved a bug in
getXYZfromHDF5
: now boxes are exported correctlysome QoL improvements behind the curtains and in the tests
added CI for documentation
merged
src/HDF5er/MDA2HDF5.py
andsrc/HDF5er/ase2HDF5.py
intosrc/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 dscribeAdded a utility for normalize SOAP vectors
Added
createReferencesFromTrajectory
that creates a variables that stores SOAP referencesset 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