crunchflow.input
================

.. py:module:: crunchflow.input

.. autoapi-nested-parse::

   
   The `crunchflow.input` subpackage provides tools for reading, writing, and modifying
   CrunchFlow input files using Python classes that mirror the structure of these files.

   CrunchFlow input files are divided into keyword blocks (e.g., `RUNTIME`, `FLOW`, `TRANSPORT`,
   `CONDITION`), each of which controls a specific aspect of the simulation setup. This
   subpackage offers Python representations for each of these blocks and supports programmatic
   workflows for creating or editing `.in` files.

   Some notable features include:
       - The `InputFile` class represents an entire CrunchFlow input file, with one attribute
         per block (e.g., `.runtime`, `.flow`, `.output`, etc.).
       - Each block is implemented as a dedicated class (e.g., `Flow`, `Transport`,
         `Condition`) and inherits from a shared `KeywordBlock` base class.
       - Input files can be generated from scratch, modified in memory, or parsed from existing
         files.
       - The `ThermoDatabase` class provides a way to read and represent CrunchFlow thermodynamic
         databases, including species and phases.

   Most blocks in a CrunchFlow input file correspond directly to attributes of the `InputFile`
   class. For example, the `FLOW` block is accessible via `InputFile.flow`, and the `RUNTIME`
   block via `InputFile.runtime`. Similarly, most keywords within a block (e.g., `calculate_flow`,
   `time_units`, or `permeability_x`) are represented as attributes of that block’s class. For
   example, `InputFile.flow.calculate_flow` or `InputFile.runtime.time_units`.

   Two notable exceptions to this structure are:
       - **Conditions**: Because multiple `CONDITION` blocks can be defined in a single input file,
         they are stored as a dictionary in `InputFile.conditions`, with each key representing the
         name of a different condition.
       - **Species in Conditions**: Within a `CONDITION` block, any number of species can be specified,
         with arbitrary names (e.g., `Na+`, `Cl-`, `HCO3-`). These are stored as key-value pairs in the
         `concentrations` dictionary of the `Condition` object, rather than as fixed attributes.















   ..
       !! processed by numpydoc !!


Subpackages
-----------

.. toctree::
   :maxdepth: 1

   /autoapi/crunchflow/input/databases/index


Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/crunchflow/input/blocks/index
   /autoapi/crunchflow/input/inputfile/index


Classes
-------

.. toctree::
   :hidden:

   /autoapi/crunchflow/input/Condition
   /autoapi/crunchflow/input/KeywordBlock
   /autoapi/crunchflow/input/AqueousDatabase
   /autoapi/crunchflow/input/AqueousReaction
   /autoapi/crunchflow/input/ThermoDatabase
   /autoapi/crunchflow/input/Exchange
   /autoapi/crunchflow/input/GasSpecies
   /autoapi/crunchflow/input/MineralKinetics
   /autoapi/crunchflow/input/Minerals
   /autoapi/crunchflow/input/PrimarySpecies
   /autoapi/crunchflow/input/SecondarySpecies
   /autoapi/crunchflow/input/SurfaceComplex
   /autoapi/crunchflow/input/SurfaceComplexParams
   /autoapi/crunchflow/input/InputFile

.. autoapisummary::

   crunchflow.input.Condition
   crunchflow.input.KeywordBlock
   crunchflow.input.AqueousDatabase
   crunchflow.input.AqueousReaction
   crunchflow.input.ThermoDatabase
   crunchflow.input.Exchange
   crunchflow.input.GasSpecies
   crunchflow.input.MineralKinetics
   crunchflow.input.Minerals
   crunchflow.input.PrimarySpecies
   crunchflow.input.SecondarySpecies
   crunchflow.input.SurfaceComplex
   crunchflow.input.SurfaceComplexParams
   crunchflow.input.InputFile