:mod:`atsim.potentials.config`
==============================

.. py:module:: atsim.potentials.config


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

Classes
~~~~~~~

.. autoapisummary::

   atsim.potentials.config.ConfigParser
   atsim.potentials.config.FilteredConfigParser
   atsim.potentials.config.Potential_Form_Registry
   atsim.potentials.config.Modifier_Registry
   atsim.potentials.config.Configuration



.. py:class:: ConfigParser(fp, overrides=[], additional=[])

   Bases: :class:`object`

   Performs initial stage (tokenizing) of generating a potential model
   suitable for tabulation functions.

   .. attribute:: pair
      

      Returns the contents of the config file's [Pair] section.

      :returns: List of tuples of (SpeciesPair, potential_form_label, params)
        Where params = [p1, p2, ..., pn] and p1 etc are the potential parameters


   .. attribute:: potential_form
      

      Return the contents of the config file's [Potential-Form] section.

      :returns: List of (PotentialFormSignature, formula_string) pairs.


   .. attribute:: tabulation
      

      Return the parsed contents of the config file's [Tabulation] section.

      This defines what type of model (pair, EAM) the config file contains and also how
      the model should be tabulated.

      :returns: _Tabulation_Section object


   .. attribute:: table_form
      

      Returns parsed content of config file's [Table-Form] section.

      This allows pre-tabulated data to be used within atsim.potentials.

      :returns: List of TableFormTuple instance tuples.


   .. attribute:: eam_embed
      

      Return the parsed contents of the configuration file's [EAM-Embed] section.

      :returns: List of (SPECIES, potential_form_label, params)
        Where params = [p1, p2, ..., pn] and p1 etc are the embedding function parameters )


   .. attribute:: eam_density
      

      Return the parsed contents of the configuration file's [EAM-Density] section.

      :returns: List of (SPECIES, potential_form_label, params)
        Where params = [p1, p2, ..., pn] and p1 etc are the density function parameters )


   .. attribute:: eam_density_fs
      

      Return the parsed contents of the configuration file's [EAM-Density] section.

      This assumes Finnis-Sinclair parsing rules. This means that SPECIES (below)
      is parsed as a `EAMFSDensitySpeciesTuple` with  `from_species` and `to_species` attributes.

      :returns: List of (SPECIES, potential_form_label, params)
        Where params = [p1, p2, ..., pn] and p1 etc are the density function parameters )


   .. attribute:: parsed_sections
      

      Returns a list of relevant sections found inside configuration file. 

      Names are returned as the `ConfigParser` attribute names which could be used to access each parsed section.
      So `[Pair]` becomes `pair` and `[EAM-Density]` is `eam_density`.

      :returns: List of attribute names representing parseable sections of the configuration file


   .. attribute:: orphan_sections
      

      Returns list of section keys, in current configuration file, that are not relevant to the `ConfigParser` class.property

      :returns: List of section labels.


   .. attribute:: raw_config_parser
      

      

   .. attribute:: species
      

      Return reference data for atomic species.

      Data is returned as a dictionary relating each species label to a dictionary mapping property name to propety value.

      :returns: Dictionary of dictionaries.


   .. method:: parse_pair_like(self, section_name)

      Parse a section as if it contains pair potentials.

      :param section_name: Name of section that should be parsed in the same way as the [Pair] section.

      :returns: List of tuples of (SpeciesPair, potential_form_label, params)
        Where params = [p1, p2, ..., pn] and p1 etc are the potential parameters



.. data:: ConfigParserOverrideTuple
   

   

.. py:exception:: ConfigOverrideException

   Bases: :class:`atsim.potentials.config._common.ConfigParserException`

   Common base class for all non-exit exceptions.


.. py:class:: FilteredConfigParser(config_parser, exclude=[], include=[])

   Bases: :class:`wrapt.ObjectProxy`

   Class that wraps around ConfigParser instances and
   filters out entries for particular, unwanted species

   .. attribute:: pair
      

      

   .. attribute:: eam_embed
      

      

   .. attribute:: eam_density
      

      

   .. attribute:: eam_density_fs
      

      


.. py:class:: Potential_Form_Registry(cfg, register_standard=False, register_pymath_functions=False)

   Bases: :class:`object`

   Factory class that takes [Potential-Form] and [Table-Form] definitions
   from ConfigParser and turns them into Potential_Form objects

   .. attribute:: registered
      

      Returns the labels for the potentials registered here.


   .. method:: __getitem__(self, k)



.. py:class:: Modifier_Registry

   Bases: :class:`object`

   Registry of factories for potential modifiers

   .. method:: __getitem__(self, k)



.. py:class:: Configuration

   Bases: :class:`object`

   Factory class that allows Tabulation objects to be built from .ini files

   .. method:: read(self, fp)

      Read potential data from the file object `fp` and return a `PairTabulation` or `EAMTabulation` object.

      :params fp: File like object containing potential information.
      :returns: Tabulation object


   .. method:: read_from_parser(self, cp)

      Read potential data from the `ConfigParser` object `cp` and return a `PairTabulation` or `EAMTabulation` instance.

      :param cp: atsim.potentials.config.ConfigParser instance.
      :returns: Tabulation object



.. py:exception:: ConfigParserException

   Bases: :class:`atsim.potentials.config._common.ConfigurationException`

   Common base class for all non-exit exceptions.


.. py:exception:: Potential_Form_Registry_Exception

   Bases: :class:`atsim.potentials.config._common.ConfigurationException`

   Common base class for all non-exit exceptions.


.. py:exception:: Potential_Form_Exception

   Bases: :class:`atsim.potentials.config._common.ConfigurationException`

   Common base class for all non-exit exceptions.