#include <ConfigIO.hh>

Inheritance diagram for CASM::ConfigIO::GradCorr:

Detailed Description

Returns correlation values.

Evaluated gradient of basis function values, w.r.t. specified DoF

Definition at line 340 of file ConfigIO.hh.

Public Types
typedef ContainerTraits< Container >::Access	Access
	Access methods for Container. More...

typedef ContainerTraits< Container >::value_type2D	ValueType

typedef DataObject	DataObject

typedef long	difference_type

typedef DataFormatterDictionary< DataObject, BaseDatumFormatter< DataObject > >	DictType

Public Member Functions
	GradCorr ()

	GradCorr (const Clexulator &clexulator)

Eigen::MatrixXd	evaluate (const Configuration &config) const override
	Returns the atom fraction. More...

std::unique_ptr< GradCorr >	clone () const
	Clone using copy constructor. More...

bool	init (const Configuration &_tmplt) const override
	If not yet initialized, use the global clexulator from the PrimClex. More...

bool	parse_args (const std::string &args) override
	Expects 'gradcorr(dof_name)', 'gradcorr(dof_name,clex_name)', 'gradcorr(dof_name,index_expression)', or 'gradcorr(dof_name,clex_name,index_expression)'. More...

virtual bool	init (const DataObject &_template_obj) const override
	Default initialization adds rules for each element. More...

virtual Index	num_passes (const DataObject &_template_obj) const override

virtual std::vector< std::string >	col_header (const DataObject &_template_obj) const override
	Default col_header uses 'name(index)' for each column. More...

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

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

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

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

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

static const std::string	Desc

Protected Types
typedef multivector< std::pair< Index, Index > >::X< 2 >	IndexContainer

Protected Member Functions
void	_parse_index_expression (const std::string &_expr)

void	_add_rule (Index row, std::pair< Index, Index > const &new_rule) const

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

const IndexContainer &	_index_rules () const

void	_prepare (DataObject const &_data_obj) const

Protected Attributes
IndexContainer	m_2D_index_rules

Private Member Functions
GradCorr *	_clone () const override
	Clone using copy constructor. More...

Private Attributes
Clexulator	m_clexulator

std::string	m_clex_name

DoFKey	m_key

DataObject const *	m_current_ptr

bool	m_known

Container	m_cache

std::string	m_name

std::string	m_description

IndexContainer	m_index_rules

const DictType *	m_home

Member Typedef Documentation

◆ Access

template<typename Container , typename DataObject >

typedef ContainerTraits<Container>::Access CASM::Base2DDatumFormatter< Container, DataObject >::Access

inherited

Access methods for Container.

Definition at line 1211 of file DataFormatterTools.hh.

◆ 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

template<typename Container , typename DataObject >

typedef multivector<std::pair<Index, Index> >::X<2> CASM::Base2DDatumFormatter< Container, DataObject >::IndexContainer

protectedinherited

Definition at line 1364 of file DataFormatterTools.hh.

◆ ValueType

template<typename Container , typename DataObject >

typedef ContainerTraits<Container>::value_type2D CASM::Base2DDatumFormatter< Container, DataObject >::ValueType

inherited

Definition at line 1212 of file DataFormatterTools.hh.

Constructor & Destructor Documentation

◆ GradCorr() [1/2]

CASM::ConfigIO::GradCorr::GradCorr ( )

inline

Definition at line 346 of file ConfigIO.hh.

◆ GradCorr() [2/2]

CASM::ConfigIO::GradCorr::GradCorr ( const Clexulator & clexulator )

inline

Definition at line 348 of file ConfigIO.hh.

Member Function Documentation

◆ _add_rule() [1/2]

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

inlineprotectedinherited

Definition at line 472 of file DataFormatter.hh.

◆ _add_rule() [2/2]

template<typename Container , typename DataObject >

void CASM::Base2DDatumFormatter< Container, DataObject >::_add_rule	(	Index	row,
		std::pair< Index, Index > const &	new_rule
	)		const

inlineprotectedinherited

Definition at line 1402 of file DataFormatterTools.hh.

◆ _clone()

GradCorr* CASM::ConfigIO::GradCorr::_clone ( ) const

inlineoverrideprivatevirtual

Clone using copy constructor.

Implements CASM::Base2DDatumFormatter< Container, DataObject >.

Definition at line 374 of file ConfigIO.hh.

◆ _index_rules()

template<typename Container , typename DataObject >

const IndexContainer& CASM::Base2DDatumFormatter< Container, DataObject >::_index_rules ( ) const

inlineprotectedinherited

Definition at line 1408 of file DataFormatterTools.hh.

◆ _parse_index_expression()

template<typename Container , typename DataObject >

void CASM::Base2DDatumFormatter< Container, DataObject >::_parse_index_expression ( const std::string & _expr )

inlineprotectedinherited

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 "5:6,4:8" by dispatching that string to BaseDatumFormatter::_parse_index_expression(), m_2D_index_rules will be populated with {{{5,4},{5,5},{5,6},{5,7},{5,8}}, {{6,4},{6,5},{6,6},{6,7},{6,8}}

Definition at line 1379 of file DataFormatterTools.hh.

◆ _prepare()

template<typename Container , typename DataObject >

void CASM::Base2DDatumFormatter< Container, DataObject >::_prepare ( DataObject const & _data_obj ) const

inlineprotectedinherited

Definition at line 1410 of file DataFormatterTools.hh.

◆ clone()

std::unique_ptr<GradCorr> CASM::ConfigIO::GradCorr::clone ( ) const

inline

Clone using copy constructor.

Definition at line 358 of file ConfigIO.hh.

◆ col_header()

template<typename Container , typename DataObject >

virtual std::vector<std::string> CASM::Base2DDatumFormatter< Container, DataObject >::col_header ( const DataObject & _template_obj ) const

inlineoverridevirtualinherited

Default col_header uses 'name(index)' for each column.

Ex: "corr(i:j,0)" "corr(i:j,1)" "corr(i:j,5)" "corr(i:j,6)"

Reimplemented from CASM::BaseDatumFormatter< DataObject >.

Definition at line 1256 of file DataFormatterTools.hh.

◆ 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.

◆ evaluate() [1/2]

Eigen::MatrixXd CASM::ConfigIO::GradCorr::evaluate ( const Configuration & config ) const

override

Returns the atom fraction.

Definition at line 411 of file ConfigIO.cc.

◆ evaluate() [2/2]

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

pure virtualinherited

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

◆ 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.

◆ init() [1/2]

bool CASM::ConfigIO::GradCorr::init ( const Configuration & _tmplt ) const

override

If not yet initialized, use the global clexulator from the PrimClex.

If not yet initialized, use the default clexulator from the PrimClex.

Definition at line 416 of file ConfigIO.cc.

◆ init() [2/2]

template<typename Container , typename DataObject >

virtual bool CASM::Base2DDatumFormatter< Container, DataObject >::init ( const DataObject & _template_obj ) const

inlineoverridevirtualinherited

Default initialization adds rules for each element.

Reimplemented from CASM::BaseDatumFormatter< DataObject >.

Definition at line 1232 of file DataFormatterTools.hh.

◆ inject()

template<typename Container , typename DataObject >

virtual void CASM::Base2DDatumFormatter< Container, DataObject >::inject	(	const DataObject &	_data_obj,
		DataStream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation injects each element.

sets DataStream::failbit if validation fails

Reimplemented from CASM::BaseValueFormatter< Container, DataObject >.

Definition at line 1290 of file DataFormatterTools.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()

template<typename Container , typename DataObject >

virtual Index CASM::Base2DDatumFormatter< Container, DataObject >::num_passes ( const DataObject & _data_obj ) const

inlineoverridevirtualinherited

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 from CASM::BaseDatumFormatter< DataObject >.

Definition at line 1237 of file DataFormatterTools.hh.

◆ operator()()

virtual Container CASM::BaseValueFormatter< Container , 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()

bool CASM::ConfigIO::GradCorr::parse_args ( const std::string & args )

overridevirtual

Expects 'gradcorr(dof_name)', 'gradcorr(dof_name,clex_name)', 'gradcorr(dof_name,index_expression)', or 'gradcorr(dof_name,clex_name,index_expression)'.

Expects 'corr', 'corr(clex_name)', 'corr(index_expression)', or 'corr(clex_name,index_expression)'.

Reimplemented from CASM::Base2DDatumFormatter< Container, DataObject >.

Definition at line 431 of file ConfigIO.cc.

◆ print()

template<typename Container , typename DataObject >

virtual void CASM::Base2DDatumFormatter< Container, DataObject >::print	(	const DataObject &	_data_obj,
		std::ostream &	_stream,
		Index	pass_index = `0`
	)		const

inlineoverridevirtualinherited

Default implementation prints each element in a column.

Prints "unknown" if validation fails

Reimplemented from CASM::BaseValueFormatter< Container, DataObject >.

Definition at line 1326 of file DataFormatterTools.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.

◆ 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.

◆ to_json()

virtual jsonParser& CASM::BaseValueFormatter< Container , 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::ConfigIO::GradCorr::Desc

static

Initial value:

=
    "Gradiant of correlation values (evaluated basis functions), with respect "
    "to a specified "
    "degree of freedom (DoF). For each configuration, output is a (D*N x C) "
    "matrix, where 'D' "
    "is DoF dimension, 'N' is either 1 (for global DoF) or number of sites in "
    "the configuration "
    "(for site DoF), and 'C' is number of basis functions. Gradient components "
    "are ordered such "
    "that components corresponding to particular site are listed in "
    "consecutive rows. Requires "
    "at least one argument, specifying the DoF with repect to which gradient "
    "is taken [e.g., 'gradcorr(disp)']. "
    "Basis functions are the basis set for the default cluster expansion, as "
    "listed by 'casm settings -l', "
    "unless otherwise specified. Accepts up to three additional arguments:\n"
    "1) a cluster expansion name, e.g. 'gradcorr(disp,formation_energy)' "
    "and/or\n"
    "2) a pair of indices, or index ranges, e.g. 'gradcorr(disp,5,2)', "
    "'gradcorr(disp,:,3:5)', 'gradcorr(disp,0:4,3)'"

Definition at line 344 of file ConfigIO.hh.

◆ m_2D_index_rules

template<typename Container , typename DataObject >

IndexContainer CASM::Base2DDatumFormatter< Container, DataObject >::m_2D_index_rules

mutableprotectedinherited

Definition at line 1366 of file DataFormatterTools.hh.

◆ m_cache

template<typename Container , typename DataObject >

Container CASM::Base2DDatumFormatter< Container, DataObject >::m_cache

mutableprivateinherited

Definition at line 1434 of file DataFormatterTools.hh.

◆ m_clex_name

std::string CASM::ConfigIO::GradCorr::m_clex_name

mutableprivate

Definition at line 377 of file ConfigIO.hh.

◆ m_clexulator

Clexulator CASM::ConfigIO::GradCorr::m_clexulator

mutableprivate

Definition at line 376 of file ConfigIO.hh.

◆ m_current_ptr

template<typename Container , typename DataObject >

DataObject const* CASM::Base2DDatumFormatter< Container, DataObject >::m_current_ptr

mutableprivateinherited

Definition at line 1432 of file DataFormatterTools.hh.

◆ m_description

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

privateinherited

Definition at line 486 of file DataFormatter.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_key

DoFKey CASM::ConfigIO::GradCorr::m_key

mutableprivate

Definition at line 378 of file ConfigIO.hh.

◆ m_known

template<typename Container , typename DataObject >

bool CASM::Base2DDatumFormatter< Container, DataObject >::m_known

mutableprivateinherited

Definition at line 1433 of file DataFormatterTools.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.

◆ Name

const std::string CASM::ConfigIO::GradCorr::Name = "gradcorr"

static

Definition at line 342 of file ConfigIO.hh.

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

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

Detailed Description

Public Types

Public Member Functions

Static Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Access

◆ DataObject

◆ DictType

◆ difference_type

◆ IndexContainer

◆ ValueType

Constructor & Destructor Documentation

◆ GradCorr() [1/2]

◆ GradCorr() [2/2]

Member Function Documentation

◆ _add_rule() [1/2]

◆ _add_rule() [2/2]

◆ _clone()

◆ _index_rules()

◆ _parse_index_expression()

◆ _prepare()

◆ clone()

◆ col_header()

◆ description()

◆ evaluate() [1/2]

◆ evaluate() [2/2]

◆ home()

◆ init() [1/2]

◆ init() [2/2]

◆ inject()

◆ long_header()

◆ name()

◆ num_passes()

◆ operator()()

◆ parse_args()

◆ print()

◆ set_home()

◆ short_header()

◆ to_json()

◆ type()

◆ validate()

Member Data Documentation

◆ Desc

◆ m_2D_index_rules

◆ m_cache

◆ m_clex_name

◆ m_clexulator

◆ m_current_ptr

◆ m_description

◆ m_home

◆ m_index_rules

◆ m_key

◆ m_known

◆ m_name

◆ Name