porereax.density
================

.. py:module:: porereax.density

.. autoapi-nested-parse::

   Module for sampling atomic and bond densities.

   The module provides:
   1. :class:`DensitySampler`: A class to sample atomic densities of specified atom structures.
   2. :class:`BondDensitySampler`: A class to sample bond densities of specified bonds.
   Both samplers support multiple dimensions for density sampling:
   - "Cartesian1D": Samples the density histogram along a specified Cartesian direction for the whole simulation box.
   - "Cartesian2D": Samples the density histogram in a specified plane for the whole simulation box.
   - "Time": Samples the number of atoms (with given bonds) or bonds per frame



Classes
-------

.. autoapisummary::

   porereax.density.DensitySampler
   porereax.density.BondDensitySampler
   porereax.density.ReactionSampler


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

.. py:class:: DensitySampler(name_out: str, atoms: list, dimension: str, region, process_id: int, atom_lib: dict, masses: dict, num_frames: int, box: numpy.ndarray, system_properties: dict, num_bins: int, direction: str, conditions: dict = {})

   Bases: :py:obj:`porereax.meta_sampler.AtomSampler`


   Sampler class for atomic densities.


   .. py:method:: sample(frame_id: int, mol_index: dict, mol_bonds: dict, bond_mask: dict, frame: object, bond_enum: object, positions_transformed: numpy.ndarray)

      Sample data for the current frame. Must be implemented by subclasses.



   .. py:method:: join_samplers(num_cores)

      Join data from multiple samplers after parallel processing.

      :param num_cores: Number of parallel processes used.
      :type num_cores: int



.. py:class:: BondDensitySampler(name_out: str, bonds: list, dimension: str, region, process_id: int, atom_lib: dict, masses: dict, num_frames: int, box: numpy.ndarray, system_properties: dict, num_bins: int, direction: str, conditions: dict = {})

   Bases: :py:obj:`porereax.meta_sampler.BondSampler`


   Sampler class for bond densities.


   .. py:method:: sample(frame_id: int, mol_index: dict, mol_bonds: dict, bond_mask: dict, frame: object, bond_enum: object, positions_transformed: numpy.ndarray)

      Sample data for the current frame. Must be implemented by subclasses.



   .. py:method:: join_samplers(num_cores: int) -> None

      Join data from multiple samplers after parallel processing.

      :param num_cores: Number of parallel processes used.
      :type num_cores: int



.. py:class:: ReactionSampler(name_out: str, reactions: list, dimension: str, region, process_id: int, atom_lib: dict, masses: dict, num_frames: int, box: numpy.ndarray, system_properties: dict, num_bins: int, direction: str, position: str)

   Bases: :py:obj:`porereax.meta_sampler.AtomSampler`


   Sampler class for reactions.


   .. py:method:: sample(frame_id: int, mol_index: dict, mol_bonds: dict, bond_mask: dict, frame: object, bond_enum: object, positions_transformed: numpy.ndarray)

      Sample data for the current frame. Must be implemented by subclasses.



   .. py:method:: join_samplers(num_cores: int) -> None

      Join data from multiple samplers after parallel processing.

      :param num_cores: Number of parallel processes used.
      :type num_cores: int