#include <ConfigMapping.hh>

Detailed Description

A class for mapping an arbitrary crystal structure as a configuration of a crystal template as described by a PrimClex. ConfigMapper manages options for the mapping algorithm and mapping cost function It also caches some information about supercell lattices so that batch imports are more efficient

Definition at line 18 of file ConfigMapping.hh.

Public Types
enum	NullInitializer { null_initializer }

enum	Options { none = 0, rotate = (1u << 0), strict = (1u << 1), robust = (1u << 2) }

Public Member Functions
	ConfigMapper (NullInitializer)
	Default construction not allowed – this constructor provides an override. More...

	ConfigMapper (PrimClex &_pclex, double _lattice_weight, double _max_volume_change=0.5, int _options=robust, double _tol=TOL)
	Construct and initialize a ConfigMapper. More...

PrimClex &	primclex () const

void	set_primclex (PrimClex &_pclex)

double	lattice_weight () const

void	set_lattice_weight (double _lw)

double	min_va_frac () const

void	set_min_va_frac (double _min_va)

double	max_va_frac () const

void	set_max_va_frac (double _max_va)

bool	import_structure_occupation (const fs::path &pos_path, std::string &imported_name, jsonParser &relaxation_properties, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op) const
	imports structure specified by 'pos_path' into primclex() by finding optimal mapping and then setting displacements and strain to zero (only the mapped occupation is preserved) More...

bool	import_structure_occupation (BasicStructure< Site > &_struc, std::string &imported_name, jsonParser &relaxation_properties, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op, bool update_struc=false) const
	imports structure specified by '_struc' into primclex() More...

bool	import_structure_occupation (BasicStructure< Site > &_struc, const Configuration *hint_ptr, std::string &imported_name, jsonParser &relaxation_properties, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op, bool update_struc=false) const
	imports structure specified by '_struc' into primclex() More...

bool	import_structure (const fs::path &pos_path, std::string &imported_name, jsonParser &relaxation_properties, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op) const
	imports structure specified by 'pos_path' into primclex() by finding optimal mapping unlike import_structure_occupation, displacements and strain are preserved More...

bool	import_structure (const BasicStructure< Site > &_struc, std::string &imported_name, jsonParser &relaxation_properties, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op) const
	imports structure specified by '_struc' into primclex() by finding optimal mapping unlike import_structure_occupation, displacements and strain are preserved More...

bool	struc_to_configdof (const BasicStructure< Site > &_struc, ConfigDoF &mapped_configdof, Lattice &mapped_lat) const
	Low-level routine to map a structure onto a ConfigDof. More...

bool	struc_to_configdof (const BasicStructure< Site > &_struc, ConfigDoF &mapped_configdof, Lattice &mapped_lat, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op, double best_cost=1e20) const
	Low-level routine to map a structure onto a ConfigDof. More...

bool	ideal_struc_to_configdof (const BasicStructure< Site > &struc, ConfigDoF &mapped_config_dof, Lattice &mapped_lat, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op) const
	Low-level routine to map a structure onto a ConfigDof if it is known to be ideal. More...

bool	deformed_struc_to_configdof (const BasicStructure< Site > &_struc, ConfigDoF &mapped_config_dof, Lattice &mapped_lat, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op, double best_cost=1e20) const
	Low-level routine to map a structure onto a ConfigDof. Does not assume structure is ideal. More...

bool	deformed_struc_to_configdof_of_lattice (const BasicStructure< Site > &struc, const Lattice &imposed_lat, double &best_cost, ConfigDoF &mapped_configdof, Lattice &mapped_lat, std::vector< Index > &best_assignment, Eigen::Matrix3d &cart_op) const
	Low-level routine to map a structure onto a ConfigDof assuming a specific Lattice, without assuming structure is ideal Will only identify mappings better than best_cost, and best_cost is updated to reflect cost of best mapping identified. More...

Private Member Functions
const std::vector< Lattice > &	_lattices_of_vol (Index prim_vol) const

Private Attributes
PrimClex *	m_pclex

std::map< Index, std::vector < Lattice > >	m_superlat_map

double	m_lattice_weight

double	m_max_volume_change

double	m_min_va_frac

double	m_max_va_frac

bool	m_robust_flag

bool	m_strict_flag

bool	m_rotate_flag

double	m_tol

std::vector< std::pair < std::string, Index > >	m_fixed_components

Constructor & Destructor Documentation

CASM::ConfigMapper::ConfigMapper ( NullInitializer )

inline

Default construction not allowed – this constructor provides an override.

Definition at line 28 of file ConfigMapping.hh.

CASM::ConfigMapper::ConfigMapper	(	PrimClex &	_pclex,
		double	_lattice_weight,
		double	_max_volume_change = `0.5`,
		int	_options = `robust`,
		double	_tol = `TOL`
	)

Construct and initialize a ConfigMapper.

Parameters

_pclex	the PrimClex that describes the crystal template
_lattice_weight	free parameter 'w' in the cost function: total_cost = wlattice_deformation+(1-w)basis_deformation can vary between 0 (completely basis-focused) and 1 (completely lattice-focused)

Parameters

_max_volume_change constrains the search space by assuming a limit on allowed volume change only taken into account when non-interstitial vacancies are allowed

Parameters

_options specify a combination of ConfigMapper::Options using bitwise OR: Ex. _options=ConfigMapper::rotate|ConfigMapper::strict Options are: 'rotate': removes rigid rotation of the imported crystal, in a least-squares sense (i.e., yields a symmetric deformation tensor) 'robust': does not assume the imported structure might be ideal ('robust' is much slower for importing ideal structures, but if 'robust' is not set and a non-ideal structure is passed, this will be almost always be detected and robust methods will be used instead. Thus, 'robust' is slightly faster if imported Structures are not ideal) 'strict': prevents transformation into canonical form. Tries to preserve original orientation of imported structure if possible

Parameters

_tol	tolerance for mapping comparisons

Definition at line 91 of file ConfigMapping.cc.

Member Function Documentation

const std::vector< Lattice > & CASM::ConfigMapper::_lattices_of_vol ( Index prim_vol ) const

private

Definition at line 743 of file ConfigMapping.cc.

bool CASM::ConfigMapper::deformed_struc_to_configdof	(	const BasicStructure< Site > &	_struc,
		ConfigDoF &	mapped_config_dof,
		Lattice &	mapped_lat,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op,
		double	best_cost = `1e20`
	)		const

Low-level routine to map a structure onto a ConfigDof. Does not assume structure is ideal.

Parameters

mapped_configdof[out]	ConfigDoF that is result of mapping procedure
mapped_lat[out]	Ideal supercell lattice (in Niggli form) of mapped configuration
best_assignment[out]	populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)
best_cost[in]	optional parameter. Method will return false of no mapping is found better than 'best_cost'

Definition at line 478 of file ConfigMapping.cc.

bool CASM::ConfigMapper::deformed_struc_to_configdof_of_lattice	(	const BasicStructure< Site > &	struc,
		const Lattice &	imposed_lat,
		double &	best_cost,
		ConfigDoF &	mapped_configdof,
		Lattice &	mapped_lat,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op
	)		const

Low-level routine to map a structure onto a ConfigDof assuming a specific Lattice, without assuming structure is ideal Will only identify mappings better than best_cost, and best_cost is updated to reflect cost of best mapping identified.

Parameters

imposed_lat[in]	Supercell Lattice onto which struc will be mapped
best_cost	Imposes an upper bound on cost of any mapping considered, and is updated to reflect best mapping encountered
mapped_configdof[out]	ConfigDoF that is result of mapping procedure
best_assignment[out]	populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)

Definition at line 624 of file ConfigMapping.cc.

bool CASM::ConfigMapper::ideal_struc_to_configdof	(	const BasicStructure< Site > &	struc,
		ConfigDoF &	mapped_config_dof,
		Lattice &	mapped_lat,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op
	)		const

Low-level routine to map a structure onto a ConfigDof if it is known to be ideal.

Parameters

mapped_configdof[out]	ConfigDoF that is result of mapping procedure
mapped_lat[out]	Ideal supercell lattice (in Niggli form) of mapped configuration
best_assignment[out]	populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)

Definition at line 420 of file ConfigMapping.cc.

bool CASM::ConfigMapper::import_structure	(	const fs::path &	pos_path,
		std::string &	imported_name,
		jsonParser &	relaxation_properties,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op
	)		const

imports structure specified by 'pos_path' into primclex() by finding optimal mapping unlike import_structure_occupation, displacements and strain are preserved

Parameters

imported_name[out] populated by the configname given to the imported structure (or an existing equivalent structure if one exists)

Parameters

relaxation_properties[out] populated by relaxation properties: 'lattice_deformation': lattice mapping score 'basis_deformation': atomic mapping score 'volume_change': V/V_ideal 'relaxation_deformation': Not recorded in this case, because it is a DoF

Parameters

best_assignment[out] populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)

Parameters

cart_op[out] populated by the cartesian isometry that rotates the imported structure onto the coordinate system of the ideal crystal

Definition at line 289 of file ConfigMapping.cc.

bool CASM::ConfigMapper::import_structure	(	const BasicStructure< Site > &	_struc,
		std::string &	imported_name,
		jsonParser &	relaxation_properties,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op
	)		const

imports structure specified by '_struc' into primclex() by finding optimal mapping unlike import_structure_occupation, displacements and strain are preserved

Definition at line 310 of file ConfigMapping.cc.

bool CASM::ConfigMapper::import_structure_occupation	(	const fs::path &	pos_path,
		std::string &	imported_name,
		jsonParser &	relaxation_properties,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op
	)		const

imports structure specified by 'pos_path' into primclex() by finding optimal mapping and then setting displacements and strain to zero (only the mapped occupation is preserved)

Parameters

imported_name	is populated by the configname given to the imported structure (or an existing equivalent structure if one exists)
relaxation_properties	is populated by relaxation properties: 'lattice_deformation': lattice mapping score 'basis_deformation': atomic mapping score 'volume_relaxation': V/V_ideal 'relaxation_deformation': 3x3 tensor describing cell relaxation
best_assignment	is populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)
cart_op	is populated by the cartesian isometry that rotates the imported structure onto the coordinate system of the ideal crystal

Definition at line 114 of file ConfigMapping.cc.

bool CASM::ConfigMapper::import_structure_occupation	(	BasicStructure< Site > &	_struc,
		std::string &	imported_name,
		jsonParser &	relaxation_properties,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op,
		bool	update_struc = `false`
	)		const

imports structure specified by '_struc' into primclex()

Parameters

update_struc if true, applies lattice similarity and/or rotation to _struc. If false, _struc is unchanged update_struc=true is useful for preserving mapping info that is lost when only the occupation is imported

Definition at line 137 of file ConfigMapping.cc.

bool CASM::ConfigMapper::import_structure_occupation	(	BasicStructure< Site > &	_struc,
		const Configuration *	hint_ptr,
		std::string &	imported_name,
		jsonParser &	relaxation_properties,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op,
		bool	update_struc = `false`
	)		const

imports structure specified by '_struc' into primclex()

Parameters

hint_ptr[in]	provides a suggestion for which Configuration _struc should map onto The hint is used to reduce search times, but may be used in the future in combination with Option 'strict' to force mapping onto a particular configuration or be used to provide user reports of the form "Suggested mapping: 0.372; Optimal mapping: 0.002"
update_struc	if true, applies lattice similarity and/or rotation to _struc. If false, _struc is unchanged update_struc=true is useful for preserving mapping info that is lost when only the occupation is imported

Definition at line 154 of file ConfigMapping.cc.

double CASM::ConfigMapper::lattice_weight ( ) const

inline

Definition at line 78 of file ConfigMapping.hh.

double CASM::ConfigMapper::max_va_frac ( ) const

inline

Definition at line 94 of file ConfigMapping.hh.

double CASM::ConfigMapper::min_va_frac ( ) const

inline

Definition at line 86 of file ConfigMapping.hh.

PrimClex& CASM::ConfigMapper::primclex ( ) const

inline

Definition at line 70 of file ConfigMapping.hh.

void CASM::ConfigMapper::set_lattice_weight ( double _lw )

inline

Definition at line 82 of file ConfigMapping.hh.

void CASM::ConfigMapper::set_max_va_frac ( double _max_va )

inline

Definition at line 98 of file ConfigMapping.hh.

void CASM::ConfigMapper::set_min_va_frac ( double _min_va )

inline

Definition at line 90 of file ConfigMapping.hh.

void CASM::ConfigMapper::set_primclex ( PrimClex & _pclex )

inline

Definition at line 74 of file ConfigMapping.hh.

bool CASM::ConfigMapper::struc_to_configdof	(	const BasicStructure< Site > &	_struc,
		ConfigDoF &	mapped_configdof,
		Lattice &	mapped_lat
	)		const

Low-level routine to map a structure onto a ConfigDof.

Parameters

mapped_configdof[out]	ConfigDoF that is result of mapping procedure
mapped_lat[out]	Ideal supercell lattice (in Niggli form) of mapped configuration

Definition at line 369 of file ConfigMapping.cc.

bool CASM::ConfigMapper::struc_to_configdof	(	const BasicStructure< Site > &	_struc,
		ConfigDoF &	mapped_configdof,
		Lattice &	mapped_lat,
		std::vector< Index > &	best_assignment,
		Eigen::Matrix3d &	cart_op,
		double	best_cost = `1e20`
	)		const

Low-level routine to map a structure onto a ConfigDof.

Parameters

mapped_configdof[out]	ConfigDoF that is result of mapping procedure
mapped_lat[out]	Ideal supercell lattice (in Niggli form) of mapped configuration
best_assignment[out]	populated by the permutation of sites in the imported structure that maps them onto sites of the ideal crystal (excluding vacancies)
best_cost[in]	optional parameter. Method will return false of no mapping is found better than 'best_cost'

Definition at line 377 of file ConfigMapping.cc.

Member Data Documentation

std::vector<std::pair<std::string, Index> > CASM::ConfigMapper::m_fixed_components

private

Definition at line 276 of file ConfigMapping.hh.

double CASM::ConfigMapper::m_lattice_weight

private

Definition at line 270 of file ConfigMapping.hh.

double CASM::ConfigMapper::m_max_va_frac

private

Definition at line 273 of file ConfigMapping.hh.

double CASM::ConfigMapper::m_max_volume_change

private

Definition at line 271 of file ConfigMapping.hh.

double CASM::ConfigMapper::m_min_va_frac

private

Definition at line 272 of file ConfigMapping.hh.

PrimClex* CASM::ConfigMapper::m_pclex

private

Definition at line 268 of file ConfigMapping.hh.

bool CASM::ConfigMapper::m_robust_flag

private

Definition at line 274 of file ConfigMapping.hh.

bool CASM::ConfigMapper::m_rotate_flag

private

Definition at line 274 of file ConfigMapping.hh.

bool CASM::ConfigMapper::m_strict_flag

private

Definition at line 274 of file ConfigMapping.hh.

std::map<Index, std::vector<Lattice> > CASM::ConfigMapper::m_superlat_map

mutableprivate

Definition at line 269 of file ConfigMapping.hh.

double CASM::ConfigMapper::m_tol

private

Definition at line 275 of file ConfigMapping.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 Types

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation