shnitsel.io.newtonx.parse
=========================

.. py:module:: shnitsel.io.newtonx.parse


Classes
-------

.. autoapisummary::

   shnitsel.io.newtonx.parse.NewtonXSettingsResult


Functions
---------

.. autoapisummary::

   shnitsel.io.newtonx.parse.parse_newtonx
   shnitsel.io.newtonx.parse.parse_settings_from_nx_log
   shnitsel.io.newtonx.parse.parse_en_data
   shnitsel.io.newtonx.parse.parse_dyn_out
   shnitsel.io.newtonx.parse.parse_nx_log_data
   shnitsel.io.newtonx.parse.parse_nx_misc_input_settings


Module Contents
---------------

.. py:function:: parse_newtonx(traj_path, loading_parameters = None)

   Function to read a NewtonX trajectory directory into a Dataset with standard shnitsel annotations and units

   :param pathlist: Path to the NewtonX trajectory output
   :type pathlist: PathOptionsType
   :param loading_parameters: Parameter settings for e.g. standard units or state names.
   :type loading_parameters: LoadingParameters | None, optional

   :returns: The Dataset object containing all of the loaded data in default shnitsel units
   :rtype: xr.Dataset


.. py:class:: NewtonXSettingsResult

   Bases: :py:obj:`NamedTuple`


   Class to keep track of key settings from the NewtonX log files


   .. py:attribute:: t_max
      :type:  float


   .. py:attribute:: delta_t
      :type:  float


   .. py:attribute:: num_steps
      :type:  int


   .. py:attribute:: num_atoms
      :type:  int


   .. py:attribute:: num_states
      :type:  int


   .. py:attribute:: completed
      :type:  bool


   .. py:attribute:: newtonx_version
      :type:  str


.. py:function:: parse_settings_from_nx_log(f)

   Function to parse key settings from the NewtonX RESULTS/nx.log file

   :param f: The input stream of lines from nx.log
   :type f: TextIOWrapper

   :returns: Key setting parameters from nx.log
             dict[str, Any]: A Dict of all relevant settings loaded from nx.log
   :rtype: NewtonXSettingsResult


.. py:function:: parse_en_data(endata_path, dataset, default_attributes)

   Function to read energy data from en.dat in case the reading from nx.log has not succeeded:

   :param endata_path: Path to a RESULTS/en.dat file
   :type endata_path: pathlib.Path
   :param dataset: The dataset to update
   :type dataset: xr.Dataset
   :param default_attributes: Default attributes for the newtonx format
   :type default_attributes: dict

   :returns: the updated dataset
   :rtype: xr.Dataset


.. py:function:: parse_dyn_out(f, dataset)

   Function to gather dynamics data (e_kin and velocities) from the RESULTS/dyn.out file, if it exists.

   :param f: The stream of lines from the dyn.out file
   :type f: TextIOWrapper
   :param dataset: The dataset to write the data to
   :type dataset: xr.Dataset

   :returns: The updated dataset after the read
   :rtype: xr.Dataset


.. py:function:: parse_nx_log_data(f, dataset, settings, default_attributes)

   Function to parse the nx.log data into a dataset from the input stream f.

   Will return the total number of actual timesteps read and the resulting dataset.
   Usual read data includes: forces, active state ("astate")

   :param f: Input filestream of a nx.log file
   :type f: TextIOWrapper
   :param dataset: The dataset to parse the data into
   :type dataset: xr.Dataset
   :param default_attributes: Default attributes for the newtonx format
   :type default_attributes: dict

   :returns: The total number of actual timesteps read and the resulting dataset after applying modifications.
   :rtype: Tuple[int, xr.Dataset]


.. py:function:: parse_nx_misc_input_settings(path)

   Function to parse various input settings from the newtonx trajectory directory.

   :param path: The path of the base trajectory folder. Should Contain `RESULTS`, `control.dyn` and either `JOB_AD` or `JOB_NAD`
   :type path: pathlib.Path

   :returns:

             The collected miscallenous settings. For specific settings, the keys "nx.log", "control.dyn"
                 allow for searching through specific settings if the files were present.
             NewtonXSettingsResult: The combined key settings if they could be extracted.
   :rtype: Dict