#include <Configuration.hh>

Inheritance diagram for CASM::Configuration:

Detailed Description

A Configuration represents the values of all degrees of freedom in a Supercell.

Definition at line 81 of file Configuration.hh.

Public Types
typedef ConfigDoF::displacement_matrix_t	displacement_matrix_t

typedef ConfigDoF::displacement_t	displacement_t

typedef ConfigDoF::const_displacement_t	const_displacement_t

Public Member Functions
	Configuration (Supercell &_supercell, const jsonParser &source=jsonParser(), const ConfigDoF &_dof=ConfigDoF())
	Construct a default Configuration. More...

	Configuration (const jsonParser &json, Supercell &_supercell, Index _id)
	Construct by reading from main data file (json) More...

void	set_multiplicity (int m)
	Construct a Configuration with occupation specified by string 'con_name'. More...

void	set_id (Index _id)

void	set_source (const jsonParser &source)

void	push_back_source (const jsonParser &source)

void	clear ()
	Clear all DoF. More...

void	init_occupation ()
	Set occupant variables to background structure. More...

void	set_occupation (const Array< int > &newoccupation)
	Set occupant variables. More...

void	set_occ (Index site_l, int val)
	Set occupant variable on site l. More...

void	clear_occupation ()
	Clear occupation. More...

void	init_displacement ()
	Set all occupant displacements to (0.,0.,0.) More...

void	set_displacement (const displacement_matrix_t &_disp)
	Set occupant displacements. More...

void	set_disp (Index site_l, const Eigen::VectorXd &_disp)
	Set occupant displacements. More...

void	clear_displacement ()
	Clear displacement. More...

void	init_deformation ()
	Set applied strain to Eigen::Matrix3d::Zero() More...

void	set_deformation (const Eigen::Matrix3d &_deformation)
	Set applied strain. More...

void	clear_deformation ()
	Clear applied strain. More...

bool	is_primitive () const
	Check if this is a primitive Configuration. More...

PermuteIterator	find_translation () const
	Returns a PermuteIterator corresponding to the first non-zero pure translation that maps the Configuration onto itself. More...

Configuration	primitive () const
	Return the primitive Configuration. More...

bool	is_canonical () const
	Check if Configuration is in the canonical form. More...

PermuteIterator	to_canonical () const
	Returns the operation that applied to *this returns the canonical form. More...

PermuteIterator	from_canonical () const
	Returns the operation that applied to the the canonical form returns *this. More...

Configuration	canonical_form () const
	Returns the canonical form Configuration in the same Supercell. More...

Configuration	in_canonical_supercell () const
	Returns the canonical form Configuration in the canonical Supercell. More...

ConfigInsertResult	insert (bool primitive_only) const
	Insert this in the canonical Supercell. More...

std::vector< PermuteIterator >	factor_group () const
	Returns the subgroup of the Supercell factor group that leaves the Configuration unchanged. More...

SymGroup	point_group () const
	Returns the point group that leaves the Configuration unchanged. More...

Configuration	fill_supercell (Supercell &scel, const SymOp &op) const
	Fills supercell 'scel' with reoriented configuration, as if by apply(op,*this) More...

Configuration	fill_supercell (Supercell &scel, const SymGroup &g) const
	Fills supercell 'scel' with reoriented configuration, as if by apply(op,*this) More...

void	set_calc_properties (const jsonParser &json)
	Read calculation results into the configuration. More...

bool	read_calc_properties (jsonParser &parsed_props) const

void	set_selected (bool _selected)

const Lattice &	ideal_lattice () const

std::string	get_id () const

int	get_multiplicity () const
	Get symmetric multiplicity (i.e., size of configuration's factor_group) More...

std::string	name () const
	SCELV_A_B_C_D_E_F/i. More...

std::string	calc_status () const

std::string	failure_type () const

const jsonParser &	source () const

fs::path	get_path () const

Index	size () const
	Returns number of sites, NOT the number of primitives that fit in here. More...

const Structure &	get_prim () const
	Get the primitive Structure for this Configuration. More...

bool	selected () const
	True if this Configuration is currently selected in the MASTER config list. More...

PrimClex &	get_primclex () const
	Get the PrimClex for this Configuration. More...

Supercell &	get_supercell () const
	Get the Supercell for this Configuration. More...

double	crystallography_tol () const
	Get the PrimClex crystallography_tol. More...

UnitCellCoord	get_uccoord (Index site_l) const
	Get the UnitCellCoord for a given linear site index. More...

int	get_b (Index site_l) const
	Get the basis site index for a given linear linear site index. More...

const ConfigDoF &	configdof () const
	const Access the DoF More...

ConfigDoF &	configdof ()
	Access the DoF. More...

bool	has_occupation () const
	True if Configuration has occupation DoF. More...

const Array< int > &	occupation () const
	Occupant variables. More...

const int &	occ (Index site_l) const
	Occupant variable on site l. More...

const Molecule &	get_mol (Index site_l) const
	Molecule on site l. More...

bool	has_displacement () const
	True if Configuration has displacement DoF. More...

const displacement_matrix_t &	displacement () const
	Occupant displacements. More...

const_displacement_t	disp (Index site_l) const
	Occupant displacement. More...

const Eigen::Matrix3d &	deformation () const
	Applied strain. More...

bool	has_deformation () const
	True if Configuration has strain DoF. More...

const Properties &	calc_properties () const

const Properties &	generated_properties () const

ReturnArray< Array< double > >	get_sublattice_composition () const

ReturnArray< Array< int > >	get_sublat_num_each_molecule () const

ReturnArray< double >	get_composition () const

ReturnArray< double >	get_true_composition () const

ReturnArray< int >	get_num_each_molecule () const
	Returns num_each_molecule[ molecule_type], where 'molecule_type' is ordered as Structure::get_struc_molecule() More...

Eigen::VectorXd	get_param_composition () const
	Returns parametric composition, as calculated using PrimClex::param_comp. More...

Eigen::VectorXd	get_num_each_component () const

Eigen::VectorXd	get_struct_fact_intensities () const

Eigen::VectorXd	get_struct_fact_intensities (const Eigen::VectorXd &component_intensities) const

void	calc_sublat_struct_fact ()

void	calc_struct_fact ()

void	calc_sublat_struct_fact (const Eigen::VectorXd &intensities)

void	calc_struct_fact (const Eigen::VectorXd &intensities)

Eigen::MatrixXcd	sublat_struct_fact ()

Eigen::MatrixXd	struct_fact ()

jsonParser &	write (jsonParser &json) const

void	write_pos () const
	Write the POS file to get_pos_path. More...

void	print (std::ostream &stream, COORD_TYPE mode, int Va_mode=0, char term= '\n', int prec=10, int pad=5) const

void	print_occupation (std::ostream &stream) const

void	print_config_list (std::ostream &stream, int composition_flag) const

void	print_composition (std::ostream &stream) const

void	print_true_composition (std::ostream &stream) const

void	print_sublattice_composition (std::ostream &stream) const

fs::path	calc_dir () const

fs::path	calc_properties_path () const

fs::path	calc_status_path () const

fs::path	get_pos_path () const
	Path to various files. More...

bool	is_equivalent (const Configuration &B) const
	Check if Configuration are equivalent wrt the prim's factor group. More...

bool	operator< (const Configuration &B) const
	Compare Configuration, via ConfigCompare. More...

bool	operator> (const Configuration &B) const

bool	operator<= (const Configuration &B) const

bool	operator>= (const Configuration &B) const

bool	operator== (const Configuration &B) const

bool	operator!= (const Configuration &B) const

Static Public Member Functions
static std::pair< std::string, Index >	split_name (std::string configname)
	Split configuration name string into scelname and config index. More...

Protected Member Functions
const Configuration &	derived () const

bool	_ne (const Configuration &B) const

Private Member Functions
int &	_occ (Index site_l)
	Convenience accessors: More...

displacement_t	_disp (Index site_l)

void	_invalidate_id ()

void	_generate_name () const

bool	_eq (const Configuration &B) const
	Equality comparison of Configuration, via ConfigEqual. More...

void	read (const jsonParser &json)
	Private members: More...

void	read_dof (const jsonParser &json)
	Functions used to perform read() More...

void	read_properties (const jsonParser &json)

jsonParser &	write_dof (jsonParser &json) const
	Functions used to perform write to config_list.json: More...

jsonParser &	write_source (jsonParser &json) const

jsonParser &	write_pos (jsonParser &json) const

jsonParser &	write_param_composition (jsonParser &json) const

jsonParser &	write_properties (jsonParser &json) const

Private Attributes
std::string	id
	Identification. More...

Supercell *	supercell
	const pointer to the (non-const) Supercell for this Configuration More...

std::shared_ptr< Supercell >	m_supercell_ptr

jsonParser	m_source
	a jsonParser object indicating where this Configuration came from More...

bool	source_updated

int	multiplicity

ConfigDoF	m_configdof
	Degrees of Freedom. More...

bool	prop_updated

Properties	calculated

Properties	generated

bool	m_selected

notstd::cloneable_ptr < FillSupercell >	m_fill_canonical
	Remember how to copy into the canonical Supercell. More...

std::string	m_name
	Remember name. More...

friend	Comparisons< Configuration >

Member Typedef Documentation

typedef ConfigDoF::const_displacement_t CASM::Configuration::const_displacement_t

Definition at line 153 of file Configuration.hh.

typedef ConfigDoF::displacement_matrix_t CASM::Configuration::displacement_matrix_t

Definition at line 151 of file Configuration.hh.

typedef ConfigDoF::displacement_t CASM::Configuration::displacement_t

Definition at line 152 of file Configuration.hh.

Constructor & Destructor Documentation

CASM::Configuration::Configuration	(	Supercell &	_supercell,
		const jsonParser &	source = `jsonParser()`,
		const ConfigDoF &	_dof = `ConfigDoF()`
	)

Construct a default Configuration.

Definition at line 36 of file Configuration.cc.

CASM::Configuration::Configuration	(	const jsonParser &	json,
		Supercell &	_supercell,
		Index	_id
	)

Construct by reading from main data file (json)

Definition at line 44 of file Configuration.cc.

Member Function Documentation

displacement_t CASM::Configuration::_disp ( Index site_l )

inlineprivate

Definition at line 617 of file Configuration.hh.

bool CASM::Configuration::_eq ( const Configuration & B ) const

private

Equality comparison of Configuration, via ConfigEqual.

Must have the same Supercell
Checks that all DoF are the same, within tolerance

Definition at line 1375 of file Configuration.cc.

void CASM::Configuration::_generate_name ( ) const

private

Definition at line 593 of file Configuration.cc.

void CASM::Configuration::_invalidate_id ( )

inlineprivate

Definition at line 621 of file Configuration.hh.

bool CASM::Comparisons< Configuration >::_ne ( const Configuration & B ) const

inlineprotectedinherited

Definition at line 56 of file Comparisons.hh.

int& CASM::Configuration::_occ ( Index site_l )

inlineprivate

Convenience accessors:

Definition at line 613 of file Configuration.hh.

fs::path CASM::Configuration::calc_dir ( ) const

Definition at line 1109 of file Configuration.cc.

const Properties & CASM::Configuration::calc_properties ( ) const

Definition at line 674 of file Configuration.cc.

fs::path CASM::Configuration::calc_properties_path ( ) const

Definition at line 1114 of file Configuration.cc.

std::string CASM::Configuration::calc_status ( ) const

Definition at line 598 of file Configuration.cc.

fs::path CASM::Configuration::calc_status_path ( ) const

Definition at line 1119 of file Configuration.cc.

void CASM::Configuration::calc_struct_fact ( )

Definition at line 1322 of file Configuration.cc.

void CASM::Configuration::calc_struct_fact ( const Eigen::VectorXd & intensities )

Structure factors are then calculated as S: S = (Q * m_phase_factor).diagonal().absolute_value() S is arranged as: [S(k1) S(k2) ... S(kn)] In the code: Q is called sublat_sf However, it would be useful to have a matrix that contained the coordinates of the k-points along with the intensities at those points. The matrix that is stored in generated is thus formatted as: [k_x k_y k_z S(k)]

Definition at line 1301 of file Configuration.cc.

void CASM::Configuration::calc_sublat_struct_fact ( )

Definition at line 1326 of file Configuration.cc.

void CASM::Configuration::calc_sublat_struct_fact ( const Eigen::VectorXd & intensities )

Calculates the sublattice structure factors as: intensities.segment<volume()>(i*volume()) * fourier_matrix = Q.column(i) Q is arranged as: [Q1(k1) Q2(k1) ... Qn(k1)] [Q1(k2) Q2(k2) ... Qn(k2)] ... [Q1(kn) Q2(kn) ... Qn(kn)] Q is called sublat_sf in the code

Definition at line 1269 of file Configuration.cc.

Configuration CASM::Configuration::canonical_form ( ) const

Returns the canonical form Configuration in the same Supercell.

Definition at line 311 of file Configuration.cc.

void CASM::Configuration::clear ( )

Clear all DoF.

This will invalidate the Configuration's id

Definition at line 125 of file Configuration.cc.

void CASM::Configuration::clear_deformation ( )

Clear applied strain.

This will invalidate the Configuration's id

Definition at line 202 of file Configuration.cc.

void CASM::Configuration::clear_displacement ( )

Clear displacement.

This will invalidate the Configuration's id

Definition at line 183 of file Configuration.cc.

void CASM::Configuration::clear_occupation ( )

Clear occupation.

This will invalidate the Configuration's id

Definition at line 155 of file Configuration.cc.

const ConfigDoF& CASM::Configuration::configdof ( ) const

inline

const Access the DoF

Definition at line 402 of file Configuration.hh.

ConfigDoF& CASM::Configuration::configdof ( )

inline

Access the DoF.

This will invalidate the Configuration's id

Definition at line 409 of file Configuration.hh.

double CASM::Configuration::crystallography_tol ( ) const

Get the PrimClex crystallography_tol.

Definition at line 654 of file Configuration.cc.

const Eigen::Matrix3d& CASM::Configuration::deformation ( ) const

inline

Applied strain.

Describes possible strains that may have been applied to the Configuration. This is the matrix that relates the reference lattice vectors to the deformed lattice vectors via

L_deformed = m_deformation * L_reference

where L is a 3x3 matrix whose columns are the lattice vectors.

Strain is applied after displacement.

Definition at line 496 of file Configuration.hh.

const Configuration & CASM::Comparisons< Configuration >::derived ( ) const

inlineprotectedinherited

Definition at line 48 of file Comparisons.hh.

const_displacement_t CASM::Configuration::disp ( Index site_l ) const

inline

Occupant displacement.

A displacement_t vector describes displacement of the occupant on site l.
Displacements are applied before strain.

Definition at line 480 of file Configuration.hh.

const displacement_matrix_t& CASM::Configuration::displacement ( ) const

inline

Occupant displacements.

A displacement_t vector for each site in the Configuration to describe displacements condensed in matrix form. This a 3xN matrix whose columns are the displacement of each of the N sites of the configuration.

Displacements are applied before strain.

Definition at line 471 of file Configuration.hh.

std::vector< PermuteIterator > CASM::Configuration::factor_group ( ) const

Returns the subgroup of the Supercell factor group that leaves the Configuration unchanged.

Definition at line 391 of file Configuration.cc.

std::string CASM::Configuration::failure_type ( ) const

Definition at line 608 of file Configuration.cc.

Configuration CASM::Configuration::fill_supercell	(	Supercell &	scel,
		const SymOp &	op
	)		const

Fills supercell 'scel' with reoriented configuration, as if by apply(op,*this)

Fills supercell 'scel' with reoriented configuration, op*(*this)

Definition at line 423 of file Configuration.cc.

Configuration CASM::Configuration::fill_supercell	(	Supercell &	scel,
		const SymGroup &	g
	)		const

Fills supercell 'scel' with reoriented configuration, as if by apply(op,*this)

Fills supercell 'scel' with reoriented configuration, op*(*this)

Uses the first symop in g that such that scel is a supercell of op*(*this)

Definition at line 436 of file Configuration.cc.

PermuteIterator CASM::Configuration::find_translation ( ) const

Returns a PermuteIterator corresponding to the first non-zero pure translation that maps the Configuration onto itself.

If primitive, returns this->get_supercell().translate_end()

Definition at line 220 of file Configuration.cc.

PermuteIterator CASM::Configuration::from_canonical ( ) const

Returns the operation that applied to the the canonical form returns *this.

Returns the operation that applied to the canonical form returns *this.

Definition at line 304 of file Configuration.cc.

const Properties & CASM::Configuration::generated_properties ( ) const

Definition at line 686 of file Configuration.cc.

int CASM::Configuration::get_b ( Index site_l ) const

Get the basis site index for a given linear linear site index.

Definition at line 664 of file Configuration.cc.

ReturnArray< double > CASM::Configuration::get_composition ( ) const

Returns composition, not counting vacancies composition[ molecule_type ]: molecule_type ordered as prim structure's get_struc_molecule(), with [Va]=0.0

get the total number of non-vacancy atoms

Definition at line 745 of file Configuration.cc.

std::string CASM::Configuration::get_id ( ) const

Definition at line 564 of file Configuration.cc.

const Molecule & CASM::Configuration::get_mol ( Index site_l ) const

Molecule on site l.

Equivalent to:

config.get_prim().basis[ config.get_b(l) ].site_occupant[ config.occupation()[l]];

Definition at line 669 of file Configuration.cc.

int CASM::Configuration::get_multiplicity ( ) const

inline

Get symmetric multiplicity (i.e., size of configuration's factor_group)

Must first be set via Configuration::set_multiplicity

Definition at line 360 of file Configuration.hh.

Eigen::VectorXd CASM::Configuration::get_num_each_component ( ) const

Returns num_each_component[ component_type] per prim cell, where 'component_type' is ordered as ParamComposition::get_components

Definition at line 810 of file Configuration.cc.

ReturnArray< int > CASM::Configuration::get_num_each_molecule ( ) const

Returns num_each_molecule[ molecule_type], where 'molecule_type' is ordered as Structure::get_struc_molecule()

Definition at line 791 of file Configuration.cc.

Eigen::VectorXd CASM::Configuration::get_param_composition ( ) const

Returns parametric composition, as calculated using PrimClex::param_comp.

Definition at line 797 of file Configuration.cc.

fs::path CASM::Configuration::get_path ( ) const

Definition at line 623 of file Configuration.cc.

fs::path CASM::Configuration::get_pos_path ( ) const

Path to various files.

Definition at line 1104 of file Configuration.cc.

const Structure & CASM::Configuration::get_prim ( ) const

Get the primitive Structure for this Configuration.

Definition at line 634 of file Configuration.cc.

PrimClex & CASM::Configuration::get_primclex ( ) const

Get the PrimClex for this Configuration.

Definition at line 644 of file Configuration.cc.

Eigen::VectorXd CASM::Configuration::get_struct_fact_intensities ( ) const

Definition at line 1246 of file Configuration.cc.

Eigen::VectorXd CASM::Configuration::get_struct_fact_intensities ( const Eigen::VectorXd & component_intensities ) const

Definition at line 1253 of file Configuration.cc.

ReturnArray< Array< int > > CASM::Configuration::get_sublat_num_each_molecule ( ) const

Returns number of each molecule by sublattice: sublat_num_each_molecule[ prim basis site / sublattice ][ molecule_type] molucule_type is ordered as in the Prim structure's site_occupant list for that basis site

Definition at line 721 of file Configuration.cc.

ReturnArray< Array< double > > CASM::Configuration::get_sublattice_composition ( ) const

Returns composition on each sublattice: sublat_comp[ prim basis site / sublattice][ molecule_type] molucule_type is ordered as in the Prim structure's site_occupant list for that basis site (includes vacancies)

Definition at line 700 of file Configuration.cc.

Supercell & CASM::Configuration::get_supercell ( ) const

Get the Supercell for this Configuration.

Definition at line 649 of file Configuration.cc.

ReturnArray< double > CASM::Configuration::get_true_composition ( ) const

Returns composition, including vacancies composition[ molecule_type ]: molecule_type ordered as prim structure's get_struc_molecule()

Definition at line 777 of file Configuration.cc.

UnitCellCoord CASM::Configuration::get_uccoord ( Index site_l ) const

Get the UnitCellCoord for a given linear site index.

Definition at line 659 of file Configuration.cc.

bool CASM::Configuration::has_deformation ( ) const

inline

True if Configuration has strain DoF.

Definition at line 501 of file Configuration.hh.

bool CASM::Configuration::has_displacement ( ) const

inline

True if Configuration has displacement DoF.

Definition at line 460 of file Configuration.hh.

bool CASM::Configuration::has_occupation ( ) const

inline

True if Configuration has occupation DoF.

Definition at line 415 of file Configuration.hh.

const Lattice & CASM::Configuration::ideal_lattice ( ) const

Definition at line 558 of file Configuration.cc.

Configuration CASM::Configuration::in_canonical_supercell ( ) const

Returns the canonical form Configuration in the canonical Supercell.

Will be a Supercell included in the PrimClex.get_supercell_list()

Definition at line 320 of file Configuration.cc.

void CASM::Configuration::init_deformation ( )

Set applied strain to Eigen::Matrix3d::Zero()

This will invalidate the Configuration's id

Definition at line 189 of file Configuration.cc.

void CASM::Configuration::init_displacement ( )

Set all occupant displacements to (0.,0.,0.)

This will invalidate the Configuration's id

Definition at line 160 of file Configuration.cc.

void CASM::Configuration::init_occupation ( )

Set occupant variables to background structure.

This will invalidate the Configuration's id

Definition at line 131 of file Configuration.cc.

ConfigInsertResult CASM::Configuration::insert ( bool primitive_only ) const

Insert this in the canonical Supercell.

Insert this configuration (in canonical form) in the canonical Supercell config list.

Parameters

primitive_only If true, only the primitive Configuration is inserted.

By convention, the primitive canonical form of a configuration must always be saved in the config list.
By default, both the primitive canonical Configuration and the equivalent non-primitive Configuration in the canonical Supercell are saved
Optionally, this can insert just the primitive Configuration

Definition at line 346 of file Configuration.cc.

bool CASM::Configuration::is_canonical ( ) const

Check if Configuration is in the canonical form.

Definition at line 281 of file Configuration.cc.

bool CASM::Configuration::is_equivalent ( const Configuration & B ) const

Check if Configuration are equivalent wrt the prim's factor group.

Equivalent to:

this->primitive() == B.primitive()

Must have the same PrimClex

Definition at line 1342 of file Configuration.cc.

bool CASM::Configuration::is_primitive ( ) const

Check if this is a primitive Configuration.

Definition at line 210 of file Configuration.cc.

std::string CASM::Configuration::name ( ) const

SCELV_A_B_C_D_E_F/i.

Returns a Configuration name.

One of the following formats:

$CANON_SCELNAME/$CANON_INDEX
- For canonical forms in canonical supercells, whether primitive or not
- CANON_INDEX will be "none" if not in config list
$PRIM_SCELNAME/$PRIM_CANON_INDEX.equiv.$FG_PERM.$TRANS_PERM
- For primitive, but non-canonical configurations in a canonical supercell
- Primitive canonical form must exist already in config list or PRIM_CANON_INDEX will be "none"
- Applies PermuteIterator(FG_PERM, TRANS_PERM) to primitive canonical configuration
$CANON_SCELNAME.$PRIM_FG_OP1/super.$PRIM_FG_OP2.$PRIM_SCELNAME/$PRIM_CANON_INDEX.equiv.$FG_PERM.$TRANS_PERM
- If the supercell is non-canonical, or the configuration is non-primitive and non-canonical
- Primitive canonical form must exist already in config list or PRIM_CANON_INDEX will be "none"
- Applies PermuteIterator(FG_PERM, TRANS_PERM) to primitive canonical configuration
- Then applies prim Structure factor group op with index PRIM_FG_OP and fills the supercell $CANON_SCELNAME.$PRIM_FG_OP1

Definition at line 586 of file Configuration.cc.

const int& CASM::Configuration::occ ( Index site_l ) const

inline

Occupant variable on site l.

The occupant on site l can be obtained from the occupation variable using:

Molecule on_site_l = config.get_prim().basis[ config.get_b(l) ].site_occupant[config.occ(l)];

For a CASM project, the occupation variables will be ordered according to the occupant DoF in a "prim.json" file. This means that for the background structure, 'occupation' is all 0

Definition at line 445 of file Configuration.hh.

const Array<int>& CASM::Configuration::occupation ( ) const

inline

Occupant variables.

With one value for each site in the Configuration, this Array describes which occupant is at each of the 'N' sites of the configuration. The occupant on site l can be obtained from the occupation variable using:

Molecule on_site_l = config.get_prim().basis[ config.get_b(l) ].site_occupant[ config.occupation()[l]];

For a CASM project, the occupation variables will be ordered according to the occupant DoF in a "prim.json" file. This means that for the background structure, 'occupation' is all 0

Definition at line 431 of file Configuration.hh.

bool CASM::Comparisons< Configuration >::operator!= ( const Configuration & B ) const

inlineinherited

Definition at line 41 of file Comparisons.hh.

bool CASM::Configuration::operator< ( const Configuration & B ) const

Compare Configuration, via ConfigCompare.

Must have the same Supercell

Definition at line 1346 of file Configuration.cc.

bool CASM::Comparisons< Configuration >::operator<= ( const Configuration & B ) const

inlineinherited

Definition at line 29 of file Comparisons.hh.

bool CASM::Comparisons< Configuration >::operator== ( const Configuration & B ) const

inlineinherited

Definition at line 37 of file Comparisons.hh.

bool CASM::Comparisons< Configuration >::operator> ( const Configuration & B ) const

inlineinherited

Definition at line 25 of file Comparisons.hh.

bool CASM::Comparisons< Configuration >::operator>= ( const Configuration & B ) const

inlineinherited

Definition at line 33 of file Comparisons.hh.

SymGroup CASM::Configuration::point_group ( ) const

Returns the point group that leaves the Configuration unchanged.

Definition at line 402 of file Configuration.cc.

Configuration CASM::Configuration::primitive ( ) const

Return the primitive Configuration.

Return a primitive Configuration.

The result holds its own Supercell, so it must be considered only a temporary Configuration

Definition at line 237 of file Configuration.cc.

void CASM::Configuration::print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		int	Va_mode = `0`,
		char	term = `'\n'`,
		int	prec = `10`,
		int	pad = `5`
	)		const

void CASM::Configuration::print_composition ( std::ostream & stream ) const

Definition at line 948 of file Configuration.cc.

void CASM::Configuration::print_config_list	(	std::ostream &	stream,
		int	composition_flag
	)		const

Definition at line 919 of file Configuration.cc.

void CASM::Configuration::print_occupation ( std::ostream & stream ) const

Definition at line 912 of file Configuration.cc.

void CASM::Configuration::print_sublattice_composition ( std::ostream & stream ) const

Definition at line 980 of file Configuration.cc.

void CASM::Configuration::print_true_composition ( std::ostream & stream ) const

Definition at line 966 of file Configuration.cc.

void CASM::Configuration::push_back_source ( const jsonParser & source )

Definition at line 81 of file Configuration.cc.

void CASM::Configuration::read ( const jsonParser & json )

private

Private members:

Reads the Configuration from the expected casm directory Uses PrimClex's current settings to read in the appropriate Properties, DeltaProperties and Correlations files if they exist

This is private, because it is only called from the constructor: Configuration(const Supercell &_supercell, Index _id) It's called from the constructor because of the Supercell pointer

Reads the Configuration from the config list Uses PrimClex's current default settings to read in the appropriate properties

This is private, because it is only called from the constructor: Configuration(const Supercell &_supercell, Index _id) It's called from the constructor because of the Supercell pointer

read dof, source, selected: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["dof"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["source"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["selected"]

read properties: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["calc"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["generated"]

Definition at line 1015 of file Configuration.cc.

bool CASM::Configuration::read_calc_properties ( jsonParser & parsed_props ) const

properties.calc.json: contains calculated properties For default clex calctype only

Definition at line 471 of file Configuration.cc.

void CASM::Configuration::read_dof ( const jsonParser & json )

private

Functions used to perform read()

Read degree of freedom, source, and selected info

read dof, source, selected: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["dof"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["source"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["selected"]

Tries to read dof from json["dof"] Tries to read source from json["source"] Tries to read selected from json["selected"]

json["dof"]: contains degree of freedom information

Definition at line 1066 of file Configuration.cc.

void CASM::Configuration::read_properties ( const jsonParser & json )

private

Read configuration properties

this does not automatically read new externally calculated properties

read properties: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["calc"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["generated"]

Tries to read calculated from json["calc"] Tries to read generated from json["gen"]

Definition at line 1093 of file Configuration.cc.

bool CASM::Configuration::selected ( ) const

inline

True if this Configuration is currently selected in the MASTER config list.

Definition at line 382 of file Configuration.hh.

void CASM::Configuration::set_calc_properties ( const jsonParser & json )

Read calculation results into the configuration.

Definition at line 464 of file Configuration.cc.

void CASM::Configuration::set_deformation ( const Eigen::Matrix3d & _deformation )

Set applied strain.

Set strain applied applied to the Configuration. This is the matrix that relates the reference lattice vectors to the deformed lattice vectors via

L_deformed = m_deformation * L_reference

where L is a 3x3 matrix whose columns are the lattice vectors.

Strain is applied after displacement.
This will invalidate the Configuration's id

Definition at line 195 of file Configuration.cc.

void CASM::Configuration::set_disp	(	Index	site_l,
		const Eigen::VectorXd &	_disp
	)

Set occupant displacements.

A displacement_t vector to describe displacement of the occupant on site l.
Displacements are applied before strain.
This will invalidate the Configuration's id

Definition at line 177 of file Configuration.cc.

void CASM::Configuration::set_displacement ( const displacement_matrix_t & _disp )

Set occupant displacements.

A displacement_t vector for each site in the Configuration to describe displacements condensed in matrix form. This a 3xN matrix whose columns are the displacement of each of the N sites of the configuration.

Displacements are applied before strain.
This will invalidate the Configuration's id

Exceptions

If	code _disp.cols() != this->size()

Definition at line 165 of file Configuration.cc.

void CASM::Configuration::set_id ( Index _id )

Definition at line 57 of file Configuration.cc.

void CASM::Configuration::set_multiplicity ( int m )

inline

Construct a Configuration with occupation specified by string 'con_name'.

set symmetric multiplicity (i.e., size of configuration's factor_group)

Definition at line 173 of file Configuration.hh.

void CASM::Configuration::set_occ	(	Index	site_l,
		int	val
	)

Set occupant variable on site l.

The occupant on site l can be obtained from the occupation variable using:

Molecule on_site_l = config.get_prim().basis[ config.get_b(l) ].site_occupant[config.occ(l)];

For a CASM project, the occupation variables will be ordered according to the occupant DoF in a "prim.json" file. This means that for the background structure, 'occupation' is all 0
No check is performed as to whether val is in the correct range
This will invalidate the Configuration's id

Definition at line 149 of file Configuration.cc.

void CASM::Configuration::set_occupation ( const Array< int > & newoccupation )

Set occupant variables.

With one value for each site in the Configuration, this Array describes which occupant is at each of the 'N' sites of the configuration. The occupant on site l can be obtained from the occupation variable using:

Molecule on_site_l = config.get_prim().basis[ config.get_b(l) ].site_occupant[ config.occupation()[l]];

For a CASM project, the occupation variables will be ordered according to the occupant DoF in a "prim.json" file. This means that for the background structure, 'occupation' is all 0
This will invalidate the Configuration's id

Exceptions

If	code newoccupation.size() != this->size()

Definition at line 136 of file Configuration.cc.

void CASM::Configuration::set_selected ( bool _selected )

inline

Definition at line 346 of file Configuration.hh.

void CASM::Configuration::set_source ( const jsonParser & source )

Definition at line 66 of file Configuration.cc.

Index CASM::Configuration::size ( ) const

Returns number of sites, NOT the number of primitives that fit in here.

Definition at line 629 of file Configuration.cc.

const jsonParser & CASM::Configuration::source ( ) const

Definition at line 618 of file Configuration.cc.

std::pair< std::string, Index > CASM::Configuration::split_name ( std::string configname )

static

Split configuration name string into scelname and config index.

Definition at line 1354 of file Configuration.cc.

Eigen::MatrixXd CASM::Configuration::struct_fact ( )

Definition at line 1330 of file Configuration.cc.

Eigen::MatrixXcd CASM::Configuration::sublat_struct_fact ( )

Definition at line 1336 of file Configuration.cc.

PermuteIterator CASM::Configuration::to_canonical ( ) const

Returns the operation that applied to *this returns the canonical form.

Definition at line 295 of file Configuration.cc.

jsonParser & CASM::Configuration::write ( jsonParser & json ) const

Writes the Configuration to the correct casm directory Uses PrimClex's current settings to write the appropriate Properties, DeltaProperties and Correlations files

Writes the Configuration to a json object (the config list) Uses PrimClex's current default settings to write the appropriate properties

'json' is a jsonParser JSON object (or will be set to a JSON object)

write_dof, source, selected: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["dof"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["source"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["selected"]

write_properties: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["calc"] json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["CURR_CALCTYPE"]["CURR_REF"]["properties"]["generated"]

write json object hierarchy if not existing

Definition at line 858 of file Configuration.cc.

jsonParser & CASM::Configuration::write_dof ( jsonParser & json ) const

private

Functions used to perform write to config_list.json:

Write config.json file containing degree of freedom info

writes dof: (absolute path in config_list) json["supercells"]["SCEL_NAME"]["CONFIG_ID"]["dof"]

adds: json["dof"]

Definition at line 1131 of file Configuration.cc.

jsonParser & CASM::Configuration::write_param_composition ( jsonParser & json ) const

private

Write param_composition.json file containing correlations location: json = supercells/SCEL_NAME/CONFIG_ID/CURR_CLEX/CURR_REF, adds: param_composition

Definition at line 1204 of file Configuration.cc.

void CASM::Configuration::write_pos ( ) const

Write the POS file to get_pos_path.

Definition at line 893 of file Configuration.cc.

jsonParser & CASM::Configuration::write_pos ( jsonParser & json ) const

private

Write POS file containing Structure location: json = supercells/SCEL_NAME/CONFIG_ID, adds: pos If the configuration is completely vacant, json["pos"] = null

Definition at line 1181 of file Configuration.cc.

jsonParser & CASM::Configuration::write_properties ( jsonParser & json ) const

private

Write properties.calc.json file containing calculated properties and param_composition location: json = supercells/SCEL_NAME/CONFIG_ID/CURR_CLEX/CURR_REF/properties, adds: calc

Definition at line 1223 of file Configuration.cc.

jsonParser & CASM::Configuration::write_source ( jsonParser & json ) const

private

Write config.json file containing degree of freedom info location: json = supercells/SCEL_NAME/CONFIG_ID, adds: source

Definition at line 1168 of file Configuration.cc.

Member Data Documentation

Properties CASM::Configuration::calculated

private

Definition at line 138 of file Configuration.hh.

friend CASM::Configuration::Comparisons< Configuration >

private

Definition at line 628 of file Configuration.hh.

Properties CASM::Configuration::generated

private

Definition at line 139 of file Configuration.hh.

std::string CASM::Configuration::id

private

Identification.

Configuration DFT data is expected in: casmroot/supercells/SCEL_NAME/CONFIG_ID/CURR_CALCTYPE/properties.calc.json POS files are written to: casmroot/supercells/SCEL_NAME/CONFIG_ID/POS

Definition at line 94 of file Configuration.hh.

ConfigDoF CASM::Configuration::m_configdof

private

Degrees of Freedom.

Definition at line 121 of file Configuration.hh.

notstd::cloneable_ptr<FillSupercell> CASM::Configuration::m_fill_canonical

mutableprivate

Remember how to copy into the canonical Supercell.

Definition at line 145 of file Configuration.hh.

std::string CASM::Configuration::m_name

mutableprivate

Remember name.

Definition at line 148 of file Configuration.hh.

bool CASM::Configuration::m_selected

private

Definition at line 142 of file Configuration.hh.

jsonParser CASM::Configuration::m_source

private

a jsonParser object indicating where this Configuration came from

Definition at line 103 of file Configuration.hh.

std::shared_ptr<Supercell> CASM::Configuration::m_supercell_ptr

private

Definition at line 100 of file Configuration.hh.

int CASM::Configuration::multiplicity

private

Definition at line 108 of file Configuration.hh.

bool CASM::Configuration::prop_updated

private

Properties Keeps track of whether the Configuration properties change since reading. Be sure to set to true in your routine if it did! PROPERTIES (AS OF 07/27/15)

Definition at line 137 of file Configuration.hh.

bool CASM::Configuration::source_updated

private

Definition at line 104 of file Configuration.hh.

Supercell* CASM::Configuration::supercell

private

const pointer to the (non-const) Supercell for this Configuration

Definition at line 97 of file Configuration.hh.

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

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

Detailed Description

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Member Data Documentation