#include <ChemicalReference.hh>

Inheritance diagram for CASM::ChemicalReference:

Detailed Description

Definition at line 39 of file ChemicalReference.hh.

Public Types
typedef std::vector< ChemicalReferenceState >	RefStateVec

typedef std::map< std::string, RefStateVec >	RefStateMap

typedef Index	size_type

typedef std::map< std::string, Eigen::VectorXd >	SpecializedRef

typedef std::function< Eigen::VectorXd(const Configuration &)>	InputFunction

typedef DataObject	DataObject

typedef long	difference_type

typedef DataFormatterDictionary< DataObject, BaseDatumFormatter< DataObject > >	DictType

Public Member Functions
	ChemicalReference (const BasicStructure &prim, const Eigen::VectorXd &_global_ref, SpecializedRef _supercell_ref=SpecializedRef(), SpecializedRef _config_ref=SpecializedRef())
	Constructor. More...

template<typename RefStateIterator >
	ChemicalReference (const BasicStructure &prim, RefStateIterator begin, RefStateIterator end, double tol)
	Construct global reference via range ChemicalReferenceState. More...

std::unique_ptr< ChemicalReference >	clone () const
	Clone. More...

const BasicStructure &	prim () const
	Get primitive BasicStructure. More...

const Eigen::VectorXd &	global () const
	const Access the global reference More...

void	set_global (const Eigen::VectorXd &ref)
	Set global hyperplane reference. More...

template<typename RefStateIterator >
void	set_global (RefStateIterator begin, RefStateIterator end, double tol)
	Set global hyperplane reference. More...

const RefStateVec &	global_ref_states () const
	const Access a map of configname to RefStateVec for Supercell specialized references More...

const std::map< std::string, Eigen::VectorXd > &	supercell () const
	const Access a map of scelname to reference for Supercell specialized references More...

void	set_supercell (const std::string &scelname, const Eigen::VectorXd &ref)
	Set hyperplane reference specialized for a Supercell. More...

template<typename RefStateIterator >
void	set_supercell (const std::string &scelname, RefStateIterator begin, RefStateIterator end, double tol)
	Set hyperplane reference specialized for a Supercell. More...

size_type	erase_supercell (const std::string &scelname)
	Erase hyperplane reference specialized for a Supercell. More...

const RefStateMap &	supercell_ref_states () const
	const Access a map of configname to RefStateVec for Supercell specialized references More...

const std::map< std::string, Eigen::VectorXd > &	config () const
	const Access a map of configname to reference for Configuration specialized references More...

void	set_config (const std::string &configname, const Eigen::VectorXd &ref)
	Set hyperplane reference specialized for a Configuration. More...

template<typename RefStateIterator >
void	set_config (const std::string &configname, RefStateIterator begin, RefStateIterator end, double tol)
	Set hyperplane reference specialized for a Configuration. More...

size_type	erase_config (const std::string &configname)
	Erase hyperplane reference specialized for a Configuration. More...

const RefStateMap &	config_ref_states () const
	const Access a map of configname to RefStateVec for Configuration specialized references More...

std::function< Eigen::VectorXd(const Configuration &)>	input () const
	Return the 'input' function that maps a Configuration to coordinates. More...

Eigen::VectorXd	input (const Configuration &config) const
	Return the 'input' coordinates that a Configuration is mapped to. More...

Eigen::VectorXd	hyperplane (const Configuration &config) const
	Return the reference hyperplane used for a particular configuration. More...

double	evaluate (const Configuration &config) const override
	Return the reference for a particular configuration. More...

virtual ValueType	evaluate (const DataObject &obj) const =0

virtual ValueType	operator() (const DataObject &obj) const
	Return requested data from obj, throwing std::runtime_error if not valid. More...

virtual void	inject (const DataObject &_data_obj, DataStream &_stream, Index pass_index=0) const override
	Default implementation injects each element, via operator<<. More...

virtual void	print (const DataObject &_data_obj, std::ostream &_stream, Index pass_index=0) const override
	Default implementation prints each element in a column, via operator<<. More...

virtual jsonParser &	to_json (const DataObject &_data_obj, jsonParser &json) const override
	Default implementation calls jsonParser& to_json(const ValueType&, jsonParser&) More...

const std::string &	name () const
	Returns a name for the formatter, which becomes the tag used for parsing. More...

const std::string &	description () const
	Returns a short description of the formatter and its allowed arguments (if any). This description is used to automatically generate help screens. More...

virtual DatumFormatterClass	type () const

const DictType &	home () const
	const Access the dictionary containing this formatter, set during DictType::lookup More...

void	set_home (const DictType &home) const
	Set the dictionary containing this formatter, set during DictType::lookup. More...

virtual bool	init (const DataObject &_template_obj) const
	Perform all initialization steps using _template_obj. Returns true if initialization is successful and false if _template_obj has insufficient data to complete initialization. More...

virtual bool	validate (const DataObject &_data_obj) const
	Returns true if _data_obj has valid values for requested data. More...

virtual std::vector< std::string >	col_header (const DataObject &_template_obj) const
	Returns a header string for each scalar produced by the formatter parsing the entries in the col_header should reproduce the exact query described by the formatter. Ex: "clex(formation_energy)" or "comp(a)", "comp(c)". More...

virtual std::string	long_header (const DataObject &_template_obj) const
	Returns a long expression for each scalar produced by the formatter parsing the long_header should reproduce the exact query described by the formatter Ex: "clex(formation_energy)" or "comp(a) comp(c)". More...

virtual std::string	short_header (const DataObject &_template_obj) const
	Returns a short expression for the formatter parsing the short_header should allow the formatter to be recreated (but the short header does not specify a subset of the elements) Ex: "clex(formation_energy)" or "comp". More...

virtual Index	num_passes (const DataObject &_data_obj) const

virtual bool	parse_args (const std::string &args)

Static Public Member Functions
template<typename RefStateIterator >
static Eigen::VectorXd	hyperplane (const BasicStructure &prim, RefStateIterator begin, RefStateIterator end, double tol)
	Convert a set of ChemicalReferenceState to a hyperplane, including checks. More...

Static Public Attributes
static const std::string	Name = "chem_ref"

static const std::string	Desc

Protected Types
typedef multivector< Index >::X< 2 >	IndexContainer

Protected Member Functions
Eigen::VectorXd &	global ()
	Access the global reference. More...

std::map< std::string, Eigen::VectorXd > &	supercell ()
	Access a map of scelname to reference for Supercell specialized references. More...

std::map< std::string, Eigen::VectorXd > &	config ()
	Access a map of configname to reference for Configuration specialized references. More...

void	_parse_index_expression (const std::string &_expr)

void	_add_rule (const std::vector< Index > &new_rule) const

const IndexContainer &	_index_rules () const

Private Member Functions
Eigen::VectorXd &	_global ()
	Access the global reference. More...

std::map< std::string, Eigen::VectorXd > &	_supercell ()
	const Access a map of scelname to reference for Supercell specialized references More...

std::map< std::string, Eigen::VectorXd > &	_config ()
	const Access a map of configname to reference for Configuration specialized references More...

ChemicalReference *	_clone () const
	Clone. More...

Static Private Member Functions
static Eigen::VectorXd	_calc_hyperplane (const BasicStructure &prim, const std::vector< std::string > &struc_mol_name, Eigen::MatrixXd N, Eigen::VectorXd E, double tol)
	Convert a set of ChemicalReferenceState to a hyperplane, including checks. More...

Private Attributes
const BasicStructure *	m_prim

RefStateVec	m_global_ref_vec

RefStateMap	m_supercell_ref_map

RefStateMap	m_config_ref_map

InputFunction	m_input

std::map< std::string, Eigen::VectorXd >	m_config_ref

std::map< std::string, Eigen::VectorXd >	m_supercell_ref

Eigen::VectorXd	m_global_ref

std::string	m_name

std::string	m_description

IndexContainer	m_index_rules

const DictType *	m_home

Member Typedef Documentation

◆ DataObject

typedef DataObject CASM::BaseDatumFormatter< DataObject >::DataObject

inherited

Definition at line 334 of file DataFormatter.hh.

◆ DictType

typedef DataFormatterDictionary<DataObject, BaseDatumFormatter<DataObject> > CASM::BaseDatumFormatter< DataObject >::DictType

inherited

Definition at line 337 of file DataFormatter.hh.

◆ difference_type

typedef long CASM::BaseDatumFormatter< DataObject >::difference_type

inherited

Definition at line 335 of file DataFormatter.hh.

◆ IndexContainer

typedef multivector<Index>::X<2> CASM::BaseDatumFormatter< DataObject >::IndexContainer

protectedinherited

Definition at line 459 of file DataFormatter.hh.

◆ InputFunction

typedef std::function<Eigen::VectorXd(const Configuration &)> CASM::HyperPlaneReferenceBase::InputFunction

inherited

Definition at line 71 of file Reference.hh.

◆ RefStateMap

typedef std::map<std::string, RefStateVec> CASM::ChemicalReference::RefStateMap

Definition at line 42 of file ChemicalReference.hh.

◆ RefStateVec

typedef std::vector<ChemicalReferenceState> CASM::ChemicalReference::RefStateVec

Definition at line 41 of file ChemicalReference.hh.

◆ size_type

typedef Index CASM::ChemicalReference::size_type

Definition at line 43 of file ChemicalReference.hh.

◆ SpecializedRef

typedef std::map<std::string, Eigen::VectorXd> CASM::HyperPlaneReferenceBase::SpecializedRef

inherited

Definition at line 70 of file Reference.hh.

Constructor & Destructor Documentation

◆ ChemicalReference() [1/2]

CASM::ChemicalReference::ChemicalReference	(	const BasicStructure &	prim,
		const Eigen::VectorXd &	_global_ref,
		SpecializedRef	_supercell_ref = `SpecializedRef()`,
		SpecializedRef	_config_ref = `SpecializedRef()`
	)

explicit

Constructor.

Parameters

_global_ref	An Eigen::VectorXd giving the intercepts of the hyperplane used for the global reference
_supercell_ref	A map of scelname to Eigen::VectorXd specializing the the reference value by Supercell
_config_ref	A map of configname to Eigen::VectorXd specializing the the reference value by Configuration

A hyperplane reference, R, maps vector species_frac, x, to output energy_per_species, y:

y = R.dot(x)

The global reference, '_global_ref', is required, but may be specialized to give a different R for a particular Supercell or Configuration via optional '_supercell_ref' and '_config_ref'.

Definition at line 145 of file ChemicalReference.cc.

◆ ChemicalReference() [2/2]

template<typename RefStateIterator >

CASM::ChemicalReference::ChemicalReference	(	const BasicStructure &	prim,
		RefStateIterator	begin,
		RefStateIterator	end,
		double	tol
	)

explicit

Construct global reference via range ChemicalReferenceState.

Definition at line 14 of file ChemicalReference_impl.hh.

Member Function Documentation

◆ _add_rule()

void CASM::BaseDatumFormatter< DataObject >::_add_rule ( const std::vector< Index > & new_rule ) const

inlineprotectedinherited

Definition at line 472 of file DataFormatter.hh.

◆ _calc_hyperplane()

Eigen::VectorXd CASM::ChemicalReference::_calc_hyperplane	(	const BasicStructure &	prim,
		const std::vector< std::string > &	struc_mol_name,
		Eigen::MatrixXd	N,
		Eigen::VectorXd	E,
		double	tol
	)

staticprivate

Convert a set of ChemicalReferenceState to a hyperplane, including checks.

Definition at line 290 of file ChemicalReference.cc.

◆ _clone()

ChemicalReference * CASM::ChemicalReference::_clone ( ) const

privatevirtual

Clone.

Reimplemented from CASM::HyperPlaneReferenceBase.

Definition at line 284 of file ChemicalReference.cc.

◆ _config()

std::map< std::string, Eigen::VectorXd > & CASM::ChemicalReference::_config ( )

private

const Access a map of configname to reference for Configuration specialized references

Definition at line 277 of file ChemicalReference.cc.

◆ _global()

Eigen::VectorXd & CASM::ChemicalReference::_global ( )

private

Access the global reference.

Definition at line 263 of file ChemicalReference.cc.

◆ _index_rules()

const IndexContainer& CASM::BaseDatumFormatter< DataObject >::_index_rules ( ) const

inlineprotectedinherited

Definition at line 476 of file DataFormatter.hh.

◆ _parse_index_expression()

void CASM::BaseDatumFormatter< DataObject >::_parse_index_expression ( const std::string & _expr )

protectedinherited

Derived DatumFormatters have some optional functionality for parsing index expressions in order to make it easy to handle ranges such as:

formatter_name(3,4:8)

in which case, DerivedDatumFormatter::parse_args() is called with the string "3,4:8" by dispatching that string to BaseDatumFormatter::_parse_index_expression(), m_index_rules will be populated with {{3,4},{3,5},{3,6},{3,7},{3,8}}

Definition at line 470 of file DataFormatter_impl.hh.

◆ _supercell()

std::map< std::string, Eigen::VectorXd > & CASM::ChemicalReference::_supercell ( )

private

const Access a map of scelname to reference for Supercell specialized references

Definition at line 270 of file ChemicalReference.cc.

◆ clone()

std::unique_ptr< ChemicalReference > CASM::ChemicalReference::clone ( ) const

Clone.

Definition at line 154 of file ChemicalReference.cc.

◆ col_header()

virtual std::vector<std::string> CASM::BaseDatumFormatter< DataObject >::col_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a header string for each scalar produced by the formatter parsing the entries in the col_header should reproduce the exact query described by the formatter. Ex: "clex(formation_energy)" or "comp(a)", "comp(c)".

Default uses short_header

Reimplemented in CASM::Base2DDatumFormatter< Container, DataObject >, CASM::Base1DDatumFormatter< Container, DataObject >, and CASM::DatumFormatterAlias< DataObject >.

Definition at line 389 of file DataFormatter.hh.

◆ config() [1/2]

std::map<std::string, Eigen::VectorXd>& CASM::HyperPlaneReferenceBase::config ( )

inlineprotectedinherited

Access a map of configname to reference for Configuration specialized references.

Definition at line 172 of file Reference.hh.

◆ config() [2/2]

const std::map< std::string, Eigen::VectorXd > & CASM::ChemicalReference::config ( ) const

const Access a map of configname to reference for Configuration specialized references

Definition at line 229 of file ChemicalReference.cc.

◆ config_ref_states()

const ChemicalReference::RefStateMap & CASM::ChemicalReference::config_ref_states ( ) const

const Access a map of configname to RefStateVec for Configuration specialized references

A configuration with a specialized reference need not have an associated RefStateVec

Definition at line 256 of file ChemicalReference.cc.

◆ description()

const std::string& CASM::BaseDatumFormatter< DataObject >::description ( ) const

inlineinherited

Returns a short description of the formatter and its allowed arguments (if any). This description is used to automatically generate help screens.

Definition at line 352 of file DataFormatter.hh.

◆ erase_config()

ChemicalReference::size_type CASM::ChemicalReference::erase_config ( const std::string & configname )

Erase hyperplane reference specialized for a Configuration.

Definition at line 244 of file ChemicalReference.cc.

◆ erase_supercell()

ChemicalReference::size_type CASM::ChemicalReference::erase_supercell ( const std::string & scelname )

Erase hyperplane reference specialized for a Supercell.

Definition at line 207 of file ChemicalReference.cc.

◆ evaluate() [1/2]

double CASM::HyperPlaneReferenceBase::evaluate ( const Configuration & config ) const

inlineoverrideinherited

Return the reference for a particular configuration.

Returns: hyperplane(config).dot(input(config));

CASM::ChemicalReference::config
const std::map< std::string, Eigen::VectorXd > & config() const
const Access a map of configname to reference for Configuration specialized references
Definition: ChemicalReference.cc:229

CASM::ChemicalReference::hyperplane
static Eigen::VectorXd hyperplane(const BasicStructure &prim, RefStateIterator begin, RefStateIterator end, double tol)
Convert a set of ChemicalReferenceState to a hyperplane, including checks.
Definition: ChemicalReference_impl.hh:81

CASM::HyperPlaneReferenceBase::input
std::function< Eigen::VectorXd(const Configuration &)> input() const
Return the 'input' function that maps a Configuration to coordinates.
Definition: Reference.hh:132

Definition at line 153 of file Reference.hh.

◆ evaluate() [2/2]

template<typename ValueType , typename DataObject >

virtual ValueType CASM::BaseValueFormatter< ValueType, DataObject >::evaluate ( const DataObject & obj ) const

pure virtualinherited

Implemented in CASM::Generic2DDatumFormatter< Container, DataObject >, CASM::Generic1DDatumFormatter< Container, DataObject >, and CASM::GenericDatumFormatter< ValueType, DataObject >.

◆ global() [1/2]

Eigen::VectorXd& CASM::HyperPlaneReferenceBase::global ( )

inlineprotectedinherited

Access the global reference.

Definition at line 160 of file Reference.hh.

◆ global() [2/2]

const Eigen::VectorXd & CASM::ChemicalReference::global ( ) const

const Access the global reference

Definition at line 165 of file ChemicalReference.cc.

◆ global_ref_states()

const ChemicalReference::RefStateVec & CASM::ChemicalReference::global_ref_states ( ) const

const Access a map of configname to RefStateVec for Supercell specialized references

There may not be global reference states (maybe only the hyperplane is known), in which case this is 'empty' / has 'size() == 0'

Definition at line 182 of file ChemicalReference.cc.

◆ home()

const DictType& CASM::BaseDatumFormatter< DataObject >::home ( ) const

inlineinherited

const Access the dictionary containing this formatter, set during DictType::lookup

Definition at line 360 of file DataFormatter.hh.

◆ hyperplane() [1/2]

template<typename RefStateIterator >

Eigen::VectorXd CASM::ChemicalReference::hyperplane	(	const BasicStructure &	prim,
		RefStateIterator	begin,
		RefStateIterator	end,
		double	tol
	)

static

Convert a set of ChemicalReferenceState to a hyperplane, including checks.

Parameters

prim	The Structure defining the composition space the reference should span
begin,end	Iterators over a range of ChemicalReferenceState
tol	Tolerance for checking that input spans the prim composition space and a solution for the hyperplane is found

Returns: Eigen::VectorXd, R, that solves: energy = R.dot(atom_frac) for each ChemicalReferenceState

Definition at line 81 of file ChemicalReference_impl.hh.

◆ hyperplane() [2/2]

Eigen::VectorXd CASM::HyperPlaneReferenceBase::hyperplane ( const Configuration & config ) const

inherited

Return the reference hyperplane used for a particular configuration.

Returns the Configuration specific hyperplane if it exists, else the Supercell specific hyperplane if it exists, else the global hyperplane.

Definition at line 20 of file Reference.cc.

◆ init()

virtual bool CASM::BaseDatumFormatter< DataObject >::init ( const DataObject & _template_obj ) const

inlinevirtualinherited

Perform all initialization steps using _template_obj. Returns true if initialization is successful and false if _template_obj has insufficient data to complete initialization.

Reimplemented in CASM::Base2DDatumFormatter< Container, DataObject >, CASM::Base1DDatumFormatter< Container, DataObject >, and CASM::DatumFormatterAlias< DataObject >.

Definition at line 376 of file DataFormatter.hh.

◆ inject()

template<typename ValueType , typename DataObject >

virtual void CASM::BaseValueFormatter< ValueType, DataObject >::inject	(	const DataObject &	_data_obj,
		DataStream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation injects each element, via operator<<.

sets DataStream::failbit if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Reimplemented in CASM::Base2DDatumFormatter< Container, DataObject >, and CASM::Base1DDatumFormatter< Container, DataObject >.

Definition at line 821 of file DataFormatterTools.hh.

◆ input() [1/2]

std::function<Eigen::VectorXd(const Configuration &)> CASM::HyperPlaneReferenceBase::input ( ) const

inlineinherited

Return the 'input' function that maps a Configuration to coordinates.

Definition at line 132 of file Reference.hh.

◆ input() [2/2]

Eigen::VectorXd CASM::HyperPlaneReferenceBase::input ( const Configuration & config ) const

inlineinherited

Return the 'input' coordinates that a Configuration is mapped to.

Definition at line 137 of file Reference.hh.

◆ long_header()

virtual std::string CASM::BaseDatumFormatter< DataObject >::long_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a long expression for each scalar produced by the formatter parsing the long_header should reproduce the exact query described by the formatter Ex: "clex(formation_energy)" or "comp(a) comp(c)".

Default uses col_header

Definition at line 399 of file DataFormatter.hh.

◆ name()

const std::string& CASM::BaseDatumFormatter< DataObject >::name ( ) const

inlineinherited

Returns a name for the formatter, which becomes the tag used for parsing.

Definition at line 347 of file DataFormatter.hh.

◆ num_passes()

virtual Index CASM::BaseDatumFormatter< DataObject >::num_passes ( const DataObject & _data_obj ) const

inlinevirtualinherited

If data must be printed on multiple rows, returns number of rows needed to output all data from _data_obj DataFormatter class will subsequently pass over _data_obj multiple times to complete printing (if necessary)

Reimplemented in CASM::Base2DDatumFormatter< Container, DataObject >, and CASM::DatumFormatterAlias< DataObject >.

Definition at line 424 of file DataFormatter.hh.

◆ operator()()

template<typename ValueType , typename DataObject >

virtual ValueType CASM::BaseValueFormatter< ValueType, DataObject >::operator() ( const DataObject & obj ) const

inlinevirtualinherited

Return requested data from obj, throwing std::runtime_error if not valid.

Definition at line 803 of file DataFormatterTools.hh.

◆ parse_args()

virtual bool CASM::BaseDatumFormatter< DataObject >::parse_args ( const std::string & args )

inlinevirtualinherited

If DatumFormatter accepts arguments, parse them here. Arguments are assumed to be passed from the command line via: formattername(argument1,argument2,...)

from which DerivedDatumFormatter::parse_args() receives the string "argument1,argument2,..." Returns true if parse is successful, false if not (e.g., takes no arguments, already initialized, malformed input, etc).

Reimplemented in CASM::ConfigIO::StrucScore, CASM::DB::Selected< ObjType >, CASM::ScelIO::ConfigCountBase, CASM::ScelIO::TransfMat, CASM::ScelIO::SupercellCheckBase< VectorXiAttribute< Supercell > >, CASM::ScelIO::SupercellCheckBase< BooleanAttribute< Supercell > >, CASM::ConfigIO::DoFStrain, CASM::ConfigIO::RelaxationStrain, CASM::ConfigIO::Novelty, CASM::ConfigIO::BaseHull< double >, CASM::ConfigIO::BaseHull< bool >, CASM::ConfigIO::Clex, CASM::ConfigIO::GradCorr, CASM::ConfigIO::PointCorr, CASM::ConfigIO::CorrContribution, CASM::ConfigIO::Corr, CASM::ConfigIO::Comp, CASM::ConfigIO_impl::MolDependent, CASM::Base2DDatumFormatter< Container, DataObject >, CASM::Base1DDatumFormatter< Container, DataObject >, CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 456 of file DataFormatter.hh.

◆ prim()

const BasicStructure & CASM::ChemicalReference::prim ( ) const

Get primitive BasicStructure.

Definition at line 159 of file ChemicalReference.cc.

◆ print()

template<typename ValueType , typename DataObject >

virtual void CASM::BaseValueFormatter< ValueType, DataObject >::print	(	const DataObject &	_data_obj,
		std::ostream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation prints each element in a column, via operator<<.

Prints "unknown" if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Reimplemented in CASM::Base2DDatumFormatter< Container, DataObject >, and CASM::Base1DDatumFormatter< Container, DataObject >.

Definition at line 833 of file DataFormatterTools.hh.

◆ set_config() [1/2]

void CASM::ChemicalReference::set_config	(	const std::string &	configname,
		const Eigen::VectorXd &	ref
	)

Set hyperplane reference specialized for a Configuration.

Erases associated RefStateVec

Definition at line 237 of file ChemicalReference.cc.

◆ set_config() [2/2]

template<typename RefStateIterator >

void CASM::ChemicalReference::set_config	(	const std::string &	configname,
		RefStateIterator	begin,
		RefStateIterator	end,
		double	tol
	)

Set hyperplane reference specialized for a Configuration.

Inserts associated RefStateVec

Definition at line 60 of file ChemicalReference_impl.hh.

◆ set_global() [1/2]

void CASM::ChemicalReference::set_global ( const Eigen::VectorXd & ref )

Set global hyperplane reference.

Erases associated RefStateVec

Definition at line 172 of file ChemicalReference.cc.

◆ set_global() [2/2]

template<typename RefStateIterator >

void CASM::ChemicalReference::set_global	(	RefStateIterator	begin,
		RefStateIterator	end,
		double	tol
	)

Set global hyperplane reference.

Parameters

prim	The Structure defining the composition space the reference should span
begin,end	Iterators over a range of ChemicalReferenceState
tol	Tolerance for checking that input spans the prim composition space and a solution for the hyperplane is found

sets global refrence to be the Eigen::VectorXd, R, that solves:

energy = R.dot(atom_frac)

CASM::energy

double energy(const Configuration &config)

Returns the energy, normalized per unit cell.

Definition: Configuration.cc:875

for each ChemicalReferenceState

Inserts associated RefStateVec

Definition at line 37 of file ChemicalReference_impl.hh.

◆ set_home()

void CASM::BaseDatumFormatter< DataObject >::set_home ( const DictType & home ) const

inlineinherited

Set the dictionary containing this formatter, set during DictType::lookup.

Definition at line 364 of file DataFormatter.hh.

◆ set_supercell() [1/2]

void CASM::ChemicalReference::set_supercell	(	const std::string &	scelname,
		const Eigen::VectorXd &	ref
	)

Set hyperplane reference specialized for a Supercell.

Erases associated RefStateVec

Definition at line 200 of file ChemicalReference.cc.

◆ set_supercell() [2/2]

template<typename RefStateIterator >

void CASM::ChemicalReference::set_supercell	(	const std::string &	scelname,
		RefStateIterator	begin,
		RefStateIterator	end,
		double	tol
	)

Set hyperplane reference specialized for a Supercell.

Inserts associated RefStateVec

Definition at line 48 of file ChemicalReference_impl.hh.

◆ short_header()

virtual std::string CASM::BaseDatumFormatter< DataObject >::short_header ( const DataObject & _template_obj ) const

inlinevirtualinherited

Returns a short expression for the formatter parsing the short_header should allow the formatter to be recreated (but the short header does not specify a subset of the elements) Ex: "clex(formation_energy)" or "comp".

Reimplemented in CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 417 of file DataFormatter.hh.

◆ supercell() [1/2]

std::map<std::string, Eigen::VectorXd>& CASM::HyperPlaneReferenceBase::supercell ( )

inlineprotectedinherited

Access a map of scelname to reference for Supercell specialized references.

Definition at line 165 of file Reference.hh.

◆ supercell() [2/2]

const std::map< std::string, Eigen::VectorXd > & CASM::ChemicalReference::supercell ( ) const

const Access a map of scelname to reference for Supercell specialized references

Definition at line 192 of file ChemicalReference.cc.

◆ supercell_ref_states()

const ChemicalReference::RefStateMap & CASM::ChemicalReference::supercell_ref_states ( ) const

const Access a map of configname to RefStateVec for Supercell specialized references

A configuration with a specialized reference need not have an associated RefStateVec

Definition at line 219 of file ChemicalReference.cc.

◆ to_json()

template<typename ValueType , typename DataObject >

virtual jsonParser& CASM::BaseValueFormatter< ValueType, DataObject >::to_json	(	const DataObject &	_data_obj,
		jsonParser &	json
	)		const

inlineoverridevirtualinherited

Default implementation calls jsonParser& to_json(const ValueType&, jsonParser&)

Does nothing if validation fails

Implements CASM::BaseDatumFormatter< DataObject >.

Definition at line 847 of file DataFormatterTools.hh.

◆ type()

virtual DatumFormatterClass CASM::BaseDatumFormatter< DataObject >::type ( ) const

inlinevirtualinherited

Reimplemented in CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 354 of file DataFormatter.hh.

◆ validate()

virtual bool CASM::BaseDatumFormatter< DataObject >::validate ( const DataObject & _data_obj ) const

inlinevirtualinherited

Returns true if _data_obj has valid values for requested data.

Default implementation always returns true

Reimplemented in CASM::Generic2DDatumFormatter< Container, DataObject >, CASM::Generic1DDatumFormatter< Container, DataObject >, CASM::GenericDatumFormatter< ValueType, DataObject >, CASM::DatumFormatterAlias< DataObject >, and CASM::DataFormatterOperator< ValueType, ArgType, DataObject >.

Definition at line 381 of file DataFormatter.hh.

Member Data Documentation

◆ Desc

const std::string CASM::ChemicalReference::Desc

static

Initial value:

=
    "Returns a reference energy as interpolated via a composition-energy "
    "hyperplane."

Definition at line 46 of file ChemicalReference.hh.

◆ m_config_ref

std::map<std::string, Eigen::VectorXd> CASM::HyperPlaneReferenceBase::m_config_ref

privateinherited

Definition at line 182 of file Reference.hh.

◆ m_config_ref_map

RefStateMap CASM::ChemicalReference::m_config_ref_map

private

Definition at line 168 of file ChemicalReference.hh.

◆ m_description

std::string CASM::BaseDatumFormatter< DataObject >::m_description

privateinherited

Definition at line 486 of file DataFormatter.hh.

◆ m_global_ref

Eigen::VectorXd CASM::HyperPlaneReferenceBase::m_global_ref

privateinherited

Definition at line 186 of file Reference.hh.

◆ m_global_ref_vec

RefStateVec CASM::ChemicalReference::m_global_ref_vec

private

Definition at line 166 of file ChemicalReference.hh.

◆ m_home

const DictType* CASM::BaseDatumFormatter< DataObject >::m_home

mutableprivateinherited

Definition at line 488 of file DataFormatter.hh.

◆ m_index_rules

IndexContainer CASM::BaseDatumFormatter< DataObject >::m_index_rules

mutableprivateinherited

Definition at line 487 of file DataFormatter.hh.

◆ m_input

InputFunction CASM::HyperPlaneReferenceBase::m_input

privateinherited

Definition at line 180 of file Reference.hh.

◆ m_name

std::string CASM::BaseDatumFormatter< DataObject >::m_name

privateinherited

{ return notstd::make_unique<DerivedDatumFormatter>(*this);}

Definition at line 485 of file DataFormatter.hh.

◆ m_prim

const BasicStructure* CASM::ChemicalReference::m_prim

private

Definition at line 162 of file ChemicalReference.hh.

◆ m_supercell_ref

std::map<std::string, Eigen::VectorXd> CASM::HyperPlaneReferenceBase::m_supercell_ref

privateinherited

Definition at line 184 of file Reference.hh.

◆ m_supercell_ref_map

RefStateMap CASM::ChemicalReference::m_supercell_ref_map

private

Definition at line 167 of file ChemicalReference.hh.

◆ Name

const std::string CASM::ChemicalReference::Name = "chem_ref"

static

Definition at line 45 of file ChemicalReference.hh.

The documentation for this class was generated from the following files:

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/ChemicalReference.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/ChemicalReference_impl.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/clex/ChemicalReference.cc

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Member Typedef Documentation

◆ DataObject

◆ DictType

◆ difference_type

◆ IndexContainer

◆ InputFunction

◆ RefStateMap

◆ RefStateVec

◆ size_type

◆ SpecializedRef

Constructor & Destructor Documentation

◆ ChemicalReference() [1/2]

◆ ChemicalReference() [2/2]

Member Function Documentation

◆ _add_rule()

◆ _calc_hyperplane()

◆ _clone()

◆ _config()

◆ _global()

◆ _index_rules()

◆ _parse_index_expression()

◆ _supercell()

◆ clone()

◆ col_header()

◆ config() [1/2]

◆ config() [2/2]

◆ config_ref_states()

◆ description()

◆ erase_config()

◆ erase_supercell()

◆ evaluate() [1/2]

◆ evaluate() [2/2]

◆ global() [1/2]

◆ global() [2/2]

◆ global_ref_states()

◆ home()

◆ hyperplane() [1/2]

◆ hyperplane() [2/2]

◆ init()

◆ inject()

◆ input() [1/2]

◆ input() [2/2]

◆ long_header()

◆ name()

◆ num_passes()

◆ operator()()

◆ parse_args()

◆ prim()

◆ print()

◆ set_config() [1/2]

◆ set_config() [2/2]

◆ set_global() [1/2]

◆ set_global() [2/2]

◆ set_home()

◆ set_supercell() [1/2]

◆ set_supercell() [2/2]

◆ short_header()

◆ supercell() [1/2]

◆ supercell() [2/2]

◆ supercell_ref_states()

◆ to_json()

◆ type()

◆ validate()

Member Data Documentation

◆ Desc

◆ m_config_ref

◆ m_config_ref_map

◆ m_description

◆ m_global_ref

◆ m_global_ref_vec