atsim.potentials.config

Package Contents

Classes

ConfigParser(fp, overrides=[], additional=[])	Performs initial stage (tokenizing) of generating a potential model
FilteredConfigParser(config_parser, exclude=[], include=[])	Class that wraps around ConfigParser instances and
Potential_Form_Registry(cfg, register_standard=False, register_pymath_functions=False)	Factory class that takes [Potential-Form] and [Table-Form] definitions
Modifier_Registry()	Registry of factories for potential modifiers
Configuration()	Factory class that allows Tabulation objects to be built from .ini files

class atsim.potentials.config.ConfigParser(fp, overrides=[], additional=[])

Bases: object

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

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

potential_form

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

Returns:List of (PotentialFormSignature, formula_string) pairs.

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

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.

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 )

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 )

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 )

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

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.

raw_config_parser

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.

parse_pair_like(self, section_name)

Parse a section as if it contains pair potentials.

Parameters: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

atsim.potentials.config.ConfigParserOverrideTuple

exception atsim.potentials.config.ConfigOverrideException

Bases: atsim.potentials.config._common.ConfigParserException

Common base class for all non-exit exceptions.

class atsim.potentials.config.FilteredConfigParser(config_parser, exclude=[], include=[])

Bases: wrapt.ObjectProxy

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

pair

eam_embed

eam_density

eam_density_fs

class atsim.potentials.config.Potential_Form_Registry(cfg, register_standard=False, register_pymath_functions=False)

Bases: object

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

registered

Returns the labels for the potentials registered here.

__getitem__(self, k)

class atsim.potentials.config.Modifier_Registry

Bases: object

Registry of factories for potential modifiers

__getitem__(self, k)

class atsim.potentials.config.Configuration

Bases: object

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

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

read_from_parser(self, cp)

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

Parameters:cp – atsim.potentials.config.ConfigParser instance. Returns:Tabulation object

exception atsim.potentials.config.ConfigParserException

Bases: atsim.potentials.config._common.ConfigurationException

Common base class for all non-exit exceptions.

exception atsim.potentials.config.Potential_Form_Registry_Exception

Bases: atsim.potentials.config._common.ConfigurationException

Common base class for all non-exit exceptions.

exception atsim.potentials.config.Potential_Form_Exception

Bases: atsim.potentials.config._common.ConfigurationException

Common base class for all non-exit exceptions.