shnitsel.core

Submodules

• shnitsel.core.ase
• shnitsel.core.datasheet
• shnitsel.core.filter_unphysical
• shnitsel.core.filtre
• shnitsel.core.geom
• shnitsel.core.indexes
• shnitsel.core.ml
• shnitsel.core.parse
• shnitsel.core.plot
• shnitsel.core.postprocess
• shnitsel.core.spectra
• shnitsel.core.xrhelpers

Functions

open_frames(path)	Opens a NetCDF4 file saved by shnitsel-tools, specially interpreting certain attributes.
save_frames(frames, path[, complevel])	Save a Dataset, presumably (but not necessarily) consisting of frames of trajectories, to a file at path.
dihedral(atXYZ, i, j, k, l, *[, deg, full])	Calculate all dihedral angles between the atoms specified.
get_per_state(frames)
get_inter_state(frames)
assign_fosc(ds)
spectra_all_times(inter_state)

Package Contents

open_frames(path)

Opens a NetCDF4 file saved by shnitsel-tools, specially interpreting certain attributes.

Parameters:

path – The path of the file to open.

Return type:

An xarray.Dataset with any MultiIndex restored.

Raises:

• FileNotFoundError – If there is is nothing at path, or path is not a file.

• ValueError (or other exception) – Raised by the underlying h5netcdf engine if the file is corrupted.

save_frames(frames, path, complevel=9)

Save a Dataset, presumably (but not necessarily) consisting of frames of trajectories, to a file at path.

Parameters:

• accessor) (frames (omit if using) – The Dataset to save

• path – The path at which to save it

• complevel – The level of gzip compression which will be applied to all variables in the Dataset, by default 9

• optional – The level of gzip compression which will be applied to all variables in the Dataset, by default 9

Notes

This function/accessor method wraps xarray.Dataset.to_netcdf() but not numpy.any().

dihedral(atXYZ, i, j, k, l, *, deg=False, full=False)

Calculate all dihedral angles between the atoms specified. The atoms specified needed be bonded.

Parameters:

• atXYZ (AtXYZ) – A DataArray of coordinates, with atom and direction dimensions

• i (int) – The four atom indices

• j (int) – The four atom indices

• k (int) – The four atom indices

• l (int) – The four atom indices

• deg (bool) – Whether to return angles in degrees (True) or radians (False), by default False

• full (bool) – Whether to return signed angles between -180° and 180° (True) or unsigned angles between 0 and 180° (False), by default False

Return type:

A DataArray containing dihedral angles

get_per_state(frames)

Parameters:

frames (Frames)

Return type:

PerState

get_inter_state(frames)

Parameters:

frames (Frames)

Return type:

InterState

assign_fosc(ds)

Parameters:

ds (xarray.Dataset)

Return type:

xarray.Dataset

spectra_all_times(inter_state)

Parameters:

inter_state (xarray.Dataset)