SOAPify.saponify

Submodule that contains the workhorse routines to apply the SOAP calculations

Functions

saponifyMultipleTrajectories(trajContainers, ...)

Calculates and stores the SOAP descriptor for all of the trajectories in the given group/file

saponifyTrajectory(trajContainer, ...[, ...])

Calculates the SOAP fingerprints for each atom in a given hdf5 trajectory
SOAPify.saponify.saponifyMultipleTrajectories(trajContainers, SOAPoutContainers, SOAPrcut, SOAPnmax, SOAPlmax, SOAPOutputChunkDim=100, SOAPnJobs=1, SOAPatomMask=None, centersMask=None, SOAP_respectPBC=True, SOAPkwargs=None, useSoapFrom='dscribe', doOverride=False, verbose=True, useType='float64')[source]

Calculates and stores the SOAP descriptor for all of the trajectories in the given group/file

saponifyMultipleTrajectories checks if any of the group contained in trajContainers is a “trajectory group” (see SOAPify.HDF5er.HDF5erUtils.isTrajectoryGroup()) and then calculates the soap fingerprints for that trajectory and saves the result in a dataset within the SOAPoutContainers group or file

SOAPatomMask and centersMask are mutually exclusive (see SOAPify.engine.getSoapEngine())

Parameters

  • trajContainers (h5py.Group|h5py.File) – The file/group that contains the trajectories

  • SOAPoutContainers (h5py.Group|h5py.File) – The file/group that will store the SOAP results

  • SOAPrcut (float) – The cutoff for local region in angstroms. Should be bigger than 1 angstrom (option passed to the desired SOAP engine). Defaults to 8.0.

  • SOAPnmax (int) – The number of radial basis functions (option passed to the desired SOAP engine). Defaults to 8.

  • SOAPlmax (int) – The maximum degree of spherical harmonics (option passed to the desired SOAP engine). Defaults to 8.

  • SOAPOutputChunkDim (int, optional) – The dimension of the chunck of data in the SOAP results dataset. Defaults to 100.

  • SOAPnJobs (int, optional) – the number of concurrent SOAP calculations (option passed to the desired SOAP engine). Defaults to 1.

  • SOAPatomMask (list[str], optional) – the symbols of the atoms whose SOAP fingerprint will be calculated (option passed to getSoapEngine). Defaults to None.

  • centersMask (Iterable, optional) – the indexes of the atoms whose SOAP fingerprint will be calculated (option passed getSoapEngine). Defaults to None.

  • SOAP_respectPBC (bool, optional) – Determines whether the system is considered to be periodic (option passed to the desired SOAP engine). Defaults to True.

  • SOAPkwargs (dict, optional) – additional keyword arguments to be passed to the selected SOAP engine. Defaults to {}.

  • useSoapFrom (KNOWNSOAPENGINES, optional) – This string determines the selected SOAP engine for the calculations. Defaults to “dscribe”.

  • doOverride (bool, optional) – if False will raise and exception if the user ask to override an already existing DataSet. Defaults to False.

  • verbose (bool, optional) – regulates the verbosity of the step by step operations. Defaults to True.

  • useType (str,optional) – The precision used to store the data. Defaults to “float64”.

SOAPify.saponify.saponifyTrajectory(trajContainer, SOAPoutContainer, SOAPrcut, SOAPnmax, SOAPlmax, SOAPOutputChunkDim=100, SOAPnJobs=1, SOAPatomMask=None, centersMask=None, SOAP_respectPBC=True, SOAPkwargs=None, useSoapFrom='dscribe', doOverride=False, verbose=True, useType='float64')[source]

Calculates the SOAP fingerprints for each atom in a given hdf5 trajectory

Works exaclty as saponifyMultipleTrajectories() except for that it calculates the fingerprints only for the passed trajectory group (see SOAPify.HDF5er.HDF5erUtils.isTrajectoryGroup()).

SOAPatomMask and centersMask are mutually exclusive (see SOAPify.engine.getSoapEngine())

Parameters

  • trajFname (str) – The name of the hdf5 file in wich the trajectory is stored

  • trajectoryGroupPath (str) – the path of the group that contains the trajectory in trajFname

  • outputFname (str) – the name of the hdf5 file that will contain the ouput or the SOAP analysis

  • exportDatasetName (str) – the name of the dataset that will contain the SOAP results, it will be saved in the group called “SOAP”

  • SOAPOutputChunkDim (int, optional) – The dimension of the chunck of data in the SOAP results dataset. Defaults to 100.

  • SOAPnJobs (int, optional) – the number of concurrent SOAP calculations (option passed to the desired SOAP engine). Defaults to 1.

  • SOAPatomMask (str, optional) – the symbols of the atoms whose SOAP fingerprint will be calculated (option passed to the desired SOAP engine). Defaults to None.

  • SOAPrcut (float, optional) – The cutoff for local region in angstroms. Should be bigger than 1 angstrom (option passed to the desired SOAP engine). Defaults to 8.0.

  • SOAPnmax (int, optional) – The number of radial basis functions (option passed to the desired SOAP engine). Defaults to 8.

  • SOAPlmax (int, optional) – The maximum degree of spherical harmonics (option passed to the desired SOAP engine). Defaults to 8.

  • SOAP_respectPBC (bool, optional) – Determines whether the system is considered to be periodic (option passed to the desired SOAP engine). Defaults to True.

  • SOAPkwargs (dict, optional) – additional keyword arguments to be passed to the SOAP engine. Defaults to {}.

  • useSoapFrom (KNOWNSOAPENGINES, optional) – This string determines the selected SOAP engine for the calculations. Defaults to “dscribe”.

  • doOverride (bool, optional) – if False will raise and exception if the user ask to override an already existing DataSet. Defaults to False.

  • verbose (bool, optional) – regulates the verbosity of the step by step operations. Defaults to True.

  • useType (str,optional) – The precision used to store the data. Defaults to “float64”.