#include <ConfigMapping.hh>

Inheritance diagram for CASM::PrimStrucMapCalculator:

Detailed Description

Definition at line 148 of file ConfigMapping.hh.

Public Member Functions
	PrimStrucMapCalculator (BasicStructure const &_prim, std::vector< xtal::SymOp > const &symgroup={}, SimpleStructure::SpeciesMode _species_mode=SimpleStructure::SpeciesMode::ATOM)

std::vector< Eigen::Vector3d >	translations (MappingNode const &_node, SimpleStructure const &child_struc) const override
	construct list of prospective mapping translations More...

virtual SimpleStructure	resolve_setting (MappingNode const &_node, SimpleStructure const &_child_struc) const override
	Creates copy of _child_struc by applying isometry, lattice transformation, translation, and site permutation of _node Result has all sites within the unit cell. After setting resolution, the lattice and sites of _child_struc match the setting of the parent structure onto which it has been mapped (as defined by '_node') More...

void	finalize (MappingNode &_node, SimpleStructure const &child_struc, bool const &symmetrize_atomic_cost=false) const override
	Calculates final mapping score and sets _node.is_valid. More...

bool	populate_cost_mat (MappingNode &_node, SimpleStructure const &child_struc) const override

void	populate_displacement (MappingNode &_node, SimpleStructure const &child_struc) const

SimpleStructure::Info const &	struc_info (SimpleStructure const &_struc) const

SimpleStructure::Info &	struc_info (SimpleStructure &_struc) const

SimpleStructure const &	parent () const

double	xtal_tol () const
	Crystallographic tolerance, for now just return CASM::TOL. More...

SymOpVector const &	point_group () const
	List of point group operations that map parent onto itself (neglecting internal translation) More...

std::vector< Eigen::Vector3d > const &	internal_translations () const
	List of internal translations that map parent onto itself. More...

std::unordered_set< Index > const &	va_allowed () const

StrucMapping::FixedSpecies const &	fixed_species () const

void	set_sym_invariant_displacement_modes (const std::vector< Eigen::MatrixXd > &_sym_invariant_displacement_modes)
	Sets the sym_invariant_modes. More...

const std::vector< Eigen::MatrixXd > &	sym_invariant_displacement_modes () const

Index	max_n_va () const
	Return maximum possible number of vacancies in underlying primitive structure. More...

std::unique_ptr< StrucMapCalculatorInterface >	clone () const
	Make an exact copy of the calculator (including any initialized members) More...

std::unique_ptr< StrucMapCalculatorInterface >	quasi_clone (SimpleStructure _parent, SymOpVector const &_factor_group={SymOp::identity()}, SimpleStructure::SpeciesMode _species_mode=SimpleStructure::SpeciesMode::ATOM, StrucMapping::AllowedSpecies _allowed_species={}) const
	Make an exact copy of the calculator (including any initialized members) More...

template<typename ExternSymOpVector >
std::unique_ptr< StrucMapCalculatorInterface >	quasi_clone (SimpleStructure _parent, ExternSymOpVector const &_factor_group={SymOp::identity()}, SimpleStructure::SpeciesMode _species_mode=SimpleStructure::SpeciesMode::ATOM, StrucMapping::AllowedSpecies _allowed_species={}) const

Protected Member Functions
void	_set_allowed_species (StrucMapping::AllowedSpecies allowed_species)

void	_set_sym_info (SymOpVector const &_factor_group)
	Sets point_group and internal_translations by breaking factor group into pure translations and rotations/rotoreflections _factor_group should be sorted in order of decreasing character. More...

StrucMapping::AllowedSpecies const &	_allowed_species () const

StrucMapping::FixedSpecies const &	_fixed_species () const

bool	_sublat_allows_va (Index b) const

std::map< std::string, Index > const &	_max_n_species () const
	maximum allowed number of each species More...

Private Member Functions
StrucMapCalculatorInterface *	_clone () const override
	Make an exact copy of the calculator (including any initialized members) More...

virtual StrucMapCalculatorInterface *	_quasi_clone (SimpleStructure _parent, SymOpVector const &_factor_group={SymOp::identity()}, SimpleStructure::SpeciesMode _species_mode=SimpleStructure::SpeciesMode::ATOM, StrucMapping::AllowedSpecies _allowed_species={}) const override
	Make an exact copy of the calculator (including any initialized members) More...

virtual bool	_assign_molecules (MappingNode &_node, SimpleStructure const &child_struc) const
	Initializes child_struc.mol_info based on child_struc.atom_info and _node. Default behavior simply copies atom_info to mol_info. More...

Private Attributes
BasicStructure	m_prim

SimpleStructure	m_parent

SymOpVector	m_point_group

std::vector< Eigen::Vector3d >	m_internal_translations

SimpleStructure::SpeciesMode	m_species_mode

StrucMapping::AllowedSpecies	m_allowed_species

StrucMapping::FixedSpecies	m_fixed_species

std::map< std::string, Index >	m_max_n_species
	maximum allowed number of each species More...

std::unordered_set< Index >	m_va_allowed

std::vector< Eigen::MatrixXd >	m_sym_invariant_displacement_modes
	vector of symmetry invariant displacement modes in the parent structure More...

Constructor & Destructor Documentation

◆ PrimStrucMapCalculator()

CASM::PrimStrucMapCalculator::PrimStrucMapCalculator	(	BasicStructure const &	_prim,
		std::vector< xtal::SymOp > const &	symgroup = `{}`,
		SimpleStructure::SpeciesMode	_species_mode = `SimpleStructure::SpeciesMode::ATOM`
	)

Definition at line 301 of file ConfigMapping.cc.

Member Function Documentation

◆ _allowed_species()

StrucMapping::AllowedSpecies const& CASM::xtal::StrucMapCalculatorInterface::_allowed_species ( ) const

inlineprotectedinherited

Definition at line 204 of file StrucMapCalculatorInterface.hh.

◆ _assign_molecules()

bool CASM::xtal::SimpleStrucMapCalculator::_assign_molecules	(	MappingNode &	_node,
		SimpleStructure const &	child_struc
	)		const

privatevirtualinherited

Initializes child_struc.mol_info based on child_struc.atom_info and _node. Default behavior simply copies atom_info to mol_info.

Definition at line 472 of file SimpleStrucMapCalculator.cc.

◆ _clone()

StrucMapCalculatorInterface* CASM::PrimStrucMapCalculator::_clone ( ) const

inlineoverrideprivatevirtual

Make an exact copy of the calculator (including any initialized members)

Reimplemented from CASM::xtal::SimpleStrucMapCalculator.

Definition at line 158 of file ConfigMapping.hh.

◆ _fixed_species()

StrucMapping::FixedSpecies const& CASM::xtal::StrucMapCalculatorInterface::_fixed_species ( ) const

inlineprotectedinherited

Definition at line 208 of file StrucMapCalculatorInterface.hh.

◆ _max_n_species()

std::map<std::string, Index> const& CASM::xtal::StrucMapCalculatorInterface::_max_n_species ( ) const

inlineprotectedinherited

maximum allowed number of each species

Definition at line 215 of file StrucMapCalculatorInterface.hh.

◆ _quasi_clone()

virtual StrucMapCalculatorInterface* CASM::xtal::SimpleStrucMapCalculator::_quasi_clone	(	SimpleStructure	_parent,
		SymOpVector const &	_factor_group = `{SymOp::identity()}`,
		SimpleStructure::SpeciesMode	_species_mode = `SimpleStructure::SpeciesMode::ATOM`,
		StrucMapping::AllowedSpecies	_allowed_species = `{}`
	)		const

inlineoverrideprivatevirtualinherited

Make an exact copy of the calculator (including any initialized members)

Implements CASM::xtal::StrucMapCalculatorInterface.

Definition at line 74 of file SimpleStrucMapCalculator.hh.

◆ _set_allowed_species()

void CASM::xtal::StrucMapCalculatorInterface::_set_allowed_species ( StrucMapping::AllowedSpecies allowed_species )

inlineprotectedinherited

Definition at line 148 of file StrucMapCalculatorInterface.hh.

◆ _set_sym_info()

void CASM::xtal::StrucMapCalculatorInterface::_set_sym_info ( SymOpVector const & _factor_group )

inlineprotectedinherited

Sets point_group and internal_translations by breaking factor group into pure translations and rotations/rotoreflections _factor_group should be sorted in order of decreasing character.

Definition at line 184 of file StrucMapCalculatorInterface.hh.

◆ _sublat_allows_va()

bool CASM::xtal::StrucMapCalculatorInterface::_sublat_allows_va ( Index b ) const

inlineprotectedinherited

Definition at line 212 of file StrucMapCalculatorInterface.hh.

◆ clone()

std::unique_ptr<StrucMapCalculatorInterface> CASM::xtal::StrucMapCalculatorInterface::clone ( ) const

inlineinherited

Make an exact copy of the calculator (including any initialized members)

Definition at line 117 of file StrucMapCalculatorInterface.hh.

◆ finalize()

void CASM::xtal::SimpleStrucMapCalculator::finalize	(	MappingNode &	_node,
		SimpleStructure const &	child_struc,
		bool const &	symmetrize_atomic_cost = `false`
	)		const

overridevirtualinherited

Calculates final mapping score and sets _node.is_valid.

Implements CASM::xtal::StrucMapCalculatorInterface.

Definition at line 231 of file SimpleStrucMapCalculator.cc.

◆ fixed_species()

StrucMapping::FixedSpecies const& CASM::xtal::StrucMapCalculatorInterface::fixed_species ( ) const

inlineinherited

Definition at line 79 of file StrucMapCalculatorInterface.hh.

◆ internal_translations()

std::vector<Eigen::Vector3d> const& CASM::xtal::StrucMapCalculatorInterface::internal_translations ( ) const

inlineinherited

List of internal translations that map parent onto itself.

Definition at line 73 of file StrucMapCalculatorInterface.hh.

◆ max_n_va()

Index CASM::xtal::StrucMapCalculatorInterface::max_n_va ( ) const

inlineinherited

Return maximum possible number of vacancies in underlying primitive structure.

Definition at line 95 of file StrucMapCalculatorInterface.hh.

◆ parent()

SimpleStructure const& CASM::xtal::StrucMapCalculatorInterface::parent ( ) const

inlineinherited

Definition at line 63 of file StrucMapCalculatorInterface.hh.

◆ point_group()

SymOpVector const& CASM::xtal::StrucMapCalculatorInterface::point_group ( ) const

inlineinherited

List of point group operations that map parent onto itself (neglecting internal translation)

Definition at line 70 of file StrucMapCalculatorInterface.hh.

◆ populate_cost_mat()

bool CASM::xtal::SimpleStrucMapCalculator::populate_cost_mat	(	MappingNode &	_node,
		SimpleStructure const &	child_struc
	)		const

overridevirtualinherited

Implements CASM::xtal::StrucMapCalculatorInterface.

Definition at line 361 of file SimpleStrucMapCalculator.cc.

◆ populate_displacement()

void CASM::xtal::SimpleStrucMapCalculator::populate_displacement	(	MappingNode &	_node,
		SimpleStructure const &	child_struc
	)		const

inherited

Definition at line 285 of file SimpleStrucMapCalculator.cc.

◆ quasi_clone() [1/2]

template<typename ExternSymOpVector >

std::unique_ptr<StrucMapCalculatorInterface> CASM::xtal::StrucMapCalculatorInterface::quasi_clone	(	SimpleStructure	_parent,
		ExternSymOpVector const &	_factor_group = `{SymOp::identity()}`,
		SimpleStructure::SpeciesMode	_species_mode = `SimpleStructure::SpeciesMode::ATOM`,
		StrucMapping::AllowedSpecies	_allowed_species = `{}`
	)		const

inlineinherited

Definition at line 135 of file StrucMapCalculatorInterface.hh.

◆ quasi_clone() [2/2]

std::unique_ptr<StrucMapCalculatorInterface> CASM::xtal::StrucMapCalculatorInterface::quasi_clone	(	SimpleStructure	_parent,
		SymOpVector const &	_factor_group = `{SymOp::identity()}`,
		SimpleStructure::SpeciesMode	_species_mode = `SimpleStructure::SpeciesMode::ATOM`,
		StrucMapping::AllowedSpecies	_allowed_species = `{}`
	)		const

inlineinherited

Make an exact copy of the calculator (including any initialized members)

Definition at line 123 of file StrucMapCalculatorInterface.hh.

◆ resolve_setting()

SimpleStructure CASM::xtal::SimpleStrucMapCalculator::resolve_setting	(	MappingNode const &	_node,
		SimpleStructure const &	_child_struc
	)		const

overridevirtualinherited

Creates copy of _child_struc by applying isometry, lattice transformation, translation, and site permutation of _node Result has all sites within the unit cell. After setting resolution, the lattice and sites of _child_struc match the setting of the parent structure onto which it has been mapped (as defined by '_node')

Creates copy of _child_struc by applying isometry, similarity, translation, and site permutation of _node Result has all sites within the unit cell.

Implements CASM::xtal::StrucMapCalculatorInterface.

Definition at line 108 of file SimpleStrucMapCalculator.cc.

◆ set_sym_invariant_displacement_modes()

void CASM::xtal::StrucMapCalculatorInterface::set_sym_invariant_displacement_modes ( const std::vector< Eigen::MatrixXd > & _sym_invariant_displacement_modes )

inlineinherited

Sets the sym_invariant_modes.

Definition at line 84 of file StrucMapCalculatorInterface.hh.

◆ struc_info() [1/2]

SimpleStructure::Info& CASM::xtal::StrucMapCalculatorInterface::struc_info ( SimpleStructure & _struc ) const

inlineinherited

Definition at line 59 of file StrucMapCalculatorInterface.hh.

◆ struc_info() [2/2]

SimpleStructure::Info const& CASM::xtal::StrucMapCalculatorInterface::struc_info ( SimpleStructure const & _struc ) const

inlineinherited

Definition at line 55 of file StrucMapCalculatorInterface.hh.

◆ sym_invariant_displacement_modes()

const std::vector<Eigen::MatrixXd>& CASM::xtal::StrucMapCalculatorInterface::sym_invariant_displacement_modes ( ) const

inlineinherited

Definition at line 89 of file StrucMapCalculatorInterface.hh.

◆ translations()

std::vector< Eigen::Vector3d > CASM::xtal::SimpleStrucMapCalculator::translations	(	MappingNode const &	_node,
		SimpleStructure const &	child_struc
	)		const

overridevirtualinherited

construct list of prospective mapping translations

Implements CASM::xtal::StrucMapCalculatorInterface.

Definition at line 28 of file SimpleStrucMapCalculator.cc.

◆ va_allowed()

std::unordered_set<Index> const& CASM::xtal::StrucMapCalculatorInterface::va_allowed ( ) const

inlineinherited

Definition at line 77 of file StrucMapCalculatorInterface.hh.

◆ xtal_tol()

double CASM::xtal::StrucMapCalculatorInterface::xtal_tol ( ) const

inlineinherited

Crystallographic tolerance, for now just return CASM::TOL.

Definition at line 66 of file StrucMapCalculatorInterface.hh.

Member Data Documentation

◆ m_allowed_species

StrucMapping::AllowedSpecies CASM::xtal::StrucMapCalculatorInterface::m_allowed_species

privateinherited

Definition at line 231 of file StrucMapCalculatorInterface.hh.

◆ m_fixed_species

StrucMapping::FixedSpecies CASM::xtal::StrucMapCalculatorInterface::m_fixed_species

privateinherited

Definition at line 233 of file StrucMapCalculatorInterface.hh.

◆ m_internal_translations

std::vector<Eigen::Vector3d> CASM::xtal::StrucMapCalculatorInterface::m_internal_translations

privateinherited

Definition at line 227 of file StrucMapCalculatorInterface.hh.

◆ m_max_n_species

std::map<std::string, Index> CASM::xtal::StrucMapCalculatorInterface::m_max_n_species

privateinherited

maximum allowed number of each species

Definition at line 236 of file StrucMapCalculatorInterface.hh.

◆ m_parent

SimpleStructure CASM::xtal::StrucMapCalculatorInterface::m_parent

privateinherited

Definition at line 220 of file StrucMapCalculatorInterface.hh.

◆ m_point_group

SymOpVector CASM::xtal::StrucMapCalculatorInterface::m_point_group

privateinherited

Definition at line 223 of file StrucMapCalculatorInterface.hh.

◆ m_prim

BasicStructure CASM::PrimStrucMapCalculator::m_prim

private

Definition at line 162 of file ConfigMapping.hh.

◆ m_species_mode

SimpleStructure::SpeciesMode CASM::xtal::StrucMapCalculatorInterface::m_species_mode

privateinherited

Definition at line 229 of file StrucMapCalculatorInterface.hh.

◆ m_sym_invariant_displacement_modes

std::vector<Eigen::MatrixXd> CASM::xtal::StrucMapCalculatorInterface::m_sym_invariant_displacement_modes

privateinherited

vector of symmetry invariant displacement modes in the parent structure

Definition at line 242 of file StrucMapCalculatorInterface.hh.

◆ m_va_allowed

std::unordered_set<Index> CASM::xtal::StrucMapCalculatorInterface::m_va_allowed

privateinherited

Definition at line 238 of file StrucMapCalculatorInterface.hh.

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

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

Detailed Description

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ PrimStrucMapCalculator()

Member Function Documentation

◆ _allowed_species()

◆ _assign_molecules()

◆ _clone()

◆ _fixed_species()

◆ _max_n_species()

◆ _quasi_clone()

◆ _set_allowed_species()

◆ _set_sym_info()

◆ _sublat_allows_va()

◆ clone()

◆ finalize()

◆ fixed_species()

◆ internal_translations()

◆ max_n_va()

◆ parent()

◆ point_group()

◆ populate_cost_mat()

◆ populate_displacement()

◆ quasi_clone() [1/2]

◆ quasi_clone() [2/2]

◆ resolve_setting()

◆ set_sym_invariant_displacement_modes()

◆ struc_info() [1/2]

◆ struc_info() [2/2]

◆ sym_invariant_displacement_modes()

◆ translations()

◆ va_allowed()

◆ xtal_tol()

Member Data Documentation

◆ m_allowed_species

◆ m_fixed_species

◆ m_internal_translations

◆ m_max_n_species

◆ m_parent

◆ m_point_group

◆ m_prim

◆ m_species_mode

◆ m_sym_invariant_displacement_modes

◆ m_va_allowed