shnitsel.core
=============

.. py:module:: shnitsel.core


Submodules
----------

.. toctree::
   :maxdepth: 1

   /api/shnitsel/core/ase/index
   /api/shnitsel/core/datasheet/index
   /api/shnitsel/core/filter_unphysical/index
   /api/shnitsel/core/filtre/index
   /api/shnitsel/core/geom/index
   /api/shnitsel/core/indexes/index
   /api/shnitsel/core/ml/index
   /api/shnitsel/core/parse/index
   /api/shnitsel/core/plot/index
   /api/shnitsel/core/postprocess/index
   /api/shnitsel/core/spectra/index
   /api/shnitsel/core/xrhelpers/index


Functions
---------

.. autoapisummary::

   shnitsel.core.open_frames
   shnitsel.core.save_frames
   shnitsel.core.dihedral
   shnitsel.core.get_per_state
   shnitsel.core.get_inter_state
   shnitsel.core.assign_fosc
   shnitsel.core.spectra_all_times


Package Contents
----------------

.. py:function:: open_frames(path)

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

   :param path: The path of the file to open.

   :rtype: An :py:class:`xarray.Dataset` with any MultiIndex restored.

   :raises FileNotFoundError: If there is is nothing at ``path``, or ``path`` is not a file.
   :raises ValueError (or other exception): Raised by the underlying `h5netcdf <https://h5netcdf.org/>`_ engine if the file is corrupted.


.. py:function:: save_frames(frames, path, complevel=9)

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

   :param frames (omit if using accessor): The ``Dataset`` to save
   :param path: The path at which to save it
   :param complevel: The level of ``gzip`` compression which will be applied to all variables in the ``Dataset``, by default 9
   :param optional: The level of ``gzip`` compression which will be applied to all variables in the ``Dataset``, by default 9

   .. rubric:: Notes

   This function/accessor method wraps :py:meth:`xarray.Dataset.to_netcdf` but not :py:func:`numpy.any`.


.. py:function:: dihedral(atXYZ, i, j, k, l, *, deg = False, full = False)

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

   :param atXYZ: A ``DataArray`` of coordinates, with ``atom`` and ``direction`` dimensions
   :param i: The four atom indices
   :param j: The four atom indices
   :param k: The four atom indices
   :param l: The four atom indices
   :param deg: Whether to return angles in degrees (True) or radians (False), by default False
   :param full: Whether to return signed angles between -180° and 180° (True) or unsigned angles between 0 and 180° (False), by default False

   :rtype: A ``DataArray`` containing dihedral angles


.. py:function:: get_per_state(frames)

.. py:function:: get_inter_state(frames)

.. py:function:: assign_fosc(ds)

.. py:function:: spectra_all_times(inter_state)