Detailed Description

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

Modules
	Configuration Enumerators
	Enumerates Configuration.

	ConfigIsEquivalent
	Methods for comparing Configurations (with the same Supercell)

Classes
class	CASM::ConfigDoF

class	CASM::ConfigMapper

class	CASM::Configuration

struct	CASM::ConfigInsertResult
	Holds results of Configuration::insert. More...

struct	CASM::RefToCanonicalPrim
	Operations that transform a canonical primitive configuration to any equivalent. More...

Typedefs
typedef ConfigCanonicalForm< HasSupercell< Comparisons< Calculable< CRTPBase< Configuration > > > > >	CASM::ConfigurationBase

Functions
Configuration	CASM::sub_configuration (std::shared_ptr< Supercell const > sub_scel_ptr, const Configuration &super_config, const UnitCell &origin=UnitCell(0, 0, 0))
	Returns the sub-configuration that fills a particular Supercell. More...

Configuration	CASM::make_configuration (const PrimClex &primclex, std::string name)
	Make Configuration from name string. More...

Eigen::VectorXd	CASM::correlations (const Configuration &config, Clexulator const &clexulator)
	Returns correlations using 'clexulator'. More...

Eigen::VectorXd	CASM::corr_contribution (Index linear_unitcell_index, const Configuration &config, Clexulator const &clexulator)
	Returns correlation contribution from a single unit cell, not normalized. More...

Eigen::VectorXd	CASM::point_corr (Index linear_unitcell_index, Index neighbor_index, const Configuration &config, Clexulator const &clexulator)
	Returns point correlations from a single site, normalized by cluster orbit size. More...

Eigen::MatrixXd	CASM::gradcorrelations (const Configuration &config, Clexulator const &clexulator, DoFKey &key)
	Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'. More...

Eigen::VectorXd	CASM::comp (const Configuration &config)
	Returns parametric composition, as calculated using PrimClex::param_comp. More...

Eigen::VectorXd	CASM::comp_n (const Configuration &config)
	Returns the composition, as number of each species per unit cell. More...

double	CASM::n_vacancy (const Configuration &config)
	Returns the vacancy composition, as number per unit cell. More...

double	CASM::n_species (const Configuration &config)
	Returns the total number species per unit cell. More...

Eigen::VectorXd	CASM::species_frac (const Configuration &config)
	Returns the composition as species fraction, with [Va] = 0.0, in the order of Structure::get_struc_molecule. More...

Eigen::VectorXd	CASM::site_frac (const Configuration &config)
	Returns the composition as site fraction, in the order of Structure::get_struc_molecule. More...

double	CASM::energy (const Configuration &config)
	Returns the energy, normalized per unit cell. More...

double	CASM::energy_per_species (const Configuration &config)
	Returns the energy, normalized per species. More...

double	CASM::reference_energy (const Configuration &config)
	Returns the reference energy, normalized per unit cell. More...

double	CASM::reference_energy_per_species (const Configuration &config)
	Returns the reference energy, normalized per species. More...

double	CASM::formation_energy (const Configuration &config)
	Returns the formation energy, normalized per unit cell. More...

double	CASM::formation_energy_per_species (const Configuration &config)
	Returns the formation energy, normalized per species. More...

double	CASM::clex_formation_energy (const Configuration &config)
	Returns the formation energy, normalized per unit cell. More...

double	CASM::clex_formation_energy_per_species (const Configuration &config)
	Returns the formation energy, normalized per species. More...

double	CASM::rms_force (const Configuration &_config)
	Root-mean-square forces of relaxed configurations, determined from DFT (eV/Angstr.) More...

double	CASM::atomic_deformation (const Configuration &_config)
	Cost function that describes the degree to which basis sites have relaxed. More...

double	CASM::lattice_deformation (const Configuration &_config)
	Cost function that describes the degree to which lattice has relaxed. More...

double	CASM::volume_relaxation (const Configuration &_config)
	Change in volume due to relaxation, expressed as the ratio V/V_0. More...

double	CASM::relaxed_magmom (const Configuration &_config)
	Returns the relaxed magnetic moment, normalized per unit cell. More...

double	CASM::relaxed_magmom_per_species (const Configuration &_config)
	Returns the relaxed magnetic moment, normalized per species. More...

Eigen::MatrixXd	CASM::relaxed_forces (const Configuration &_config)
	relaxed forces of configuration, determined from DFT (eV/Angstr.), as a 3xN matrix More...

IntegralCluster	CASM::config_diff (const Configuration &_config1, const Configuration &_config2)
	Returns an Integral Cluster representing the perturbed sites between the configs. More...

Configuration	CASM::closest_setting (const Configuration &_config1, const Configuration &_config2)

Configuration	CASM::config_clip (const Configuration &_config, const Configuration &_bg, IntegralCluster &_clust)
	Returns a Configuration with the sites in _clust clipped from _config and placed in _bg. More...

bool	CASM::is_primitive (const Configuration &_config)
	returns true if _config describes primitive cell of the configuration it describes More...

bool	CASM::is_canonical (const Configuration &_config)
	returns true if no symmetry transformation applied to _config will increase its lexicographic order More...

bool	CASM::is_diff_trans_endpoint (const Configuration &_config)
	returns true if _config is an endpoint of any existing diff_trans_config More...

std::string	CASM::diff_trans_endpoint_of (const Configuration &_config)
	returns which diff_trans _config is an endpoint of More...

bool	CASM::has_energy (const Configuration &_config)

bool	CASM::has_reference_energy (const Configuration &_config)

bool	CASM::has_formation_energy (const Configuration &_config)

bool	CASM::has_rms_force (const Configuration &_config)

bool	CASM::has_atomic_deformation (const Configuration &_config)

bool	CASM::has_lattice_deformation (const Configuration &_config)

bool	CASM::has_volume_relaxation (const Configuration &_config)

bool	CASM::has_relaxed_magmom (const Configuration &_config)

bool	CASM::has_relaxed_mag_basis (const Configuration &_config)

Eigen::VectorXd	CASM::correlations (const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list. More...

Eigen::VectorXd	CASM::corr_contribution (Index linear_unitcell_index, const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns correlation contribution from a single unit cell, not normalized. More...

Eigen::VectorXd	CASM::point_corr (Index linear_unitcell_index, Index neighbor_index, const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns point correlations from a single site, normalized by cluster orbit size. More...

Eigen::MatrixXd	CASM::gradcorrelations (const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator, DoFKey &key)
	Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'. More...

Eigen::VectorXi	CASM::num_each_molecule (const ConfigDoF &configdof, const Supercell &scel)
	Returns num_each_molecule(molecule_type), where 'molecule_type' is ordered as Structure::get_struc_molecule() More...

Eigen::VectorXd	CASM::comp_n (const ConfigDoF &configdof, const Supercell &scel)
	Returns comp_n, the number of each molecule per primitive cell, ordered as Structure::get_struc_molecule() More...

Typedef Documentation

◆ ConfigurationBase

typedef ConfigCanonicalForm< HasSupercell<Comparisons<Calculable<CRTPBase<Configuration> > > > > CASM::ConfigurationBase

Definition at line 51 of file Configuration.hh.

Function Documentation

◆ atomic_deformation()

double CASM::atomic_deformation ( const Configuration & _config )

Cost function that describes the degree to which basis sites have relaxed.

Definition at line 935 of file Configuration.cc.

◆ clex_formation_energy()

double CASM::clex_formation_energy ( const Configuration & config )

Returns the formation energy, normalized per unit cell.

Definition at line 910 of file Configuration.cc.

◆ clex_formation_energy_per_species()

double CASM::clex_formation_energy_per_species ( const Configuration & config )

Returns the formation energy, normalized per species.

Returns the formation energy, normalized per unit cell.

Definition at line 929 of file Configuration.cc.

◆ closest_setting()

Configuration CASM::closest_setting	(	const Configuration &	_config1,
		const Configuration &	_config2
	)

Returns a rotated/translated version of config 2 that leaves it closest to the occupation of config1

Definition at line 996 of file Configuration.cc.

◆ comp()

Eigen::VectorXd CASM::comp ( const Configuration & config )

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

Definition at line 832 of file Configuration.cc.

◆ comp_n() [1/2]

Eigen::VectorXd CASM::comp_n	(	const ConfigDoF &	configdof,
		const Supercell &	scel
	)

Returns comp_n, the number of each molecule per primitive cell, ordered as Structure::get_struc_molecule()

Returns comp_n, the number of each molecule per primitive cell, ordered as Structure::xtal::struc_molecule_name()

Definition at line 1301 of file Configuration.cc.

◆ comp_n() [2/2]

Eigen::VectorXd CASM::comp_n ( const Configuration & config )

Returns the composition, as number of each species per unit cell.

Definition at line 837 of file Configuration.cc.

◆ config_clip()

Configuration CASM::config_clip	(	const Configuration &	_config,
		const Configuration &	_bg,
		IntegralCluster &	_clust
	)

Returns a Configuration with the sites in _clust clipped from _config and placed in _bg.

Definition at line 1024 of file Configuration.cc.

◆ config_diff()

IntegralCluster CASM::config_diff	(	const Configuration &	_config1,
		const Configuration &	_config2
	)

Returns an Integral Cluster representing the perturbed sites between the configs.

Returns an IntegralCluster representing the perturbation between the configs.

Definition at line 978 of file Configuration.cc.

◆ corr_contribution() [1/2]

Eigen::VectorXd CASM::corr_contribution	(	Index	linear_unitcell_index,
		const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator const &	clexulator
	)

Returns correlation contribution from a single unit cell, not normalized.

Supercell needs a correctly populated neighbor list.

Definition at line 1147 of file Configuration.cc.

◆ corr_contribution() [2/2]

Eigen::VectorXd CASM::corr_contribution	(	Index	linear_unitcell_index,
		const Configuration &	config,
		Clexulator const &	clexulator
	)

Returns correlation contribution from a single unit cell, not normalized.

Returns correlations using 'clexulator'.

Definition at line 807 of file Configuration.cc.

◆ correlations() [1/2]

Eigen::VectorXd CASM::correlations	(	const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator const &	clexulator
	)

Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list.

Definition at line 1116 of file Configuration.cc.

◆ correlations() [2/2]

Eigen::VectorXd CASM::correlations	(	const Configuration &	config,
		Clexulator const &	clexulator
	)

Returns correlations using 'clexulator'.

Definition at line 801 of file Configuration.cc.

◆ diff_trans_endpoint_of()

std::string CASM::diff_trans_endpoint_of ( const Configuration & _config )

returns which diff_trans _config is an endpoint of

◆ energy()

double CASM::energy ( const Configuration & config )

Returns the energy, normalized per unit cell.

Definition at line 875 of file Configuration.cc.

◆ energy_per_species()

double CASM::energy_per_species ( const Configuration & config )

Returns the energy, normalized per species.

Definition at line 881 of file Configuration.cc.

◆ formation_energy()

double CASM::formation_energy ( const Configuration & config )

Returns the formation energy, normalized per unit cell.

Definition at line 898 of file Configuration.cc.

◆ formation_energy_per_species()

double CASM::formation_energy_per_species ( const Configuration & config )

Returns the formation energy, normalized per species.

Currently, this is really a Molecule fraction

Definition at line 905 of file Configuration.cc.

◆ gradcorrelations() [1/2]

Eigen::MatrixXd CASM::gradcorrelations	(	const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator const &	clexulator,
		DoFKey &	key
	)

Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'.

Definition at line 1197 of file Configuration.cc.

◆ gradcorrelations() [2/2]

Eigen::MatrixXd CASM::gradcorrelations	(	const Configuration &	config,
		Clexulator const &	clexulator,
		DoFKey &	key
	)

Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'.

Definition at line 825 of file Configuration.cc.

◆ has_atomic_deformation()

bool CASM::has_atomic_deformation ( const Configuration & _config )

Definition at line 1074 of file Configuration.cc.

◆ has_energy()

bool CASM::has_energy ( const Configuration & _config )

Definition at line 1055 of file Configuration.cc.

◆ has_formation_energy()

bool CASM::has_formation_energy ( const Configuration & _config )

Definition at line 1064 of file Configuration.cc.

◆ has_lattice_deformation()

bool CASM::has_lattice_deformation ( const Configuration & _config )

Definition at line 1078 of file Configuration.cc.

◆ has_reference_energy()

bool CASM::has_reference_energy ( const Configuration & _config )

Definition at line 1059 of file Configuration.cc.

◆ has_relaxed_mag_basis()

bool CASM::has_relaxed_mag_basis ( const Configuration & _config )

Definition at line 1090 of file Configuration.cc.

◆ has_relaxed_magmom()

bool CASM::has_relaxed_magmom ( const Configuration & _config )

Definition at line 1086 of file Configuration.cc.

◆ has_rms_force()

bool CASM::has_rms_force ( const Configuration & _config )

Definition at line 1068 of file Configuration.cc.

◆ has_volume_relaxation()

bool CASM::has_volume_relaxation ( const Configuration & _config )

Definition at line 1082 of file Configuration.cc.

◆ is_canonical()

bool CASM::is_canonical ( const Configuration & _config )

returns true if no symmetry transformation applied to _config will increase its lexicographic order

Definition at line 1051 of file Configuration.cc.

◆ is_diff_trans_endpoint()

bool CASM::is_diff_trans_endpoint ( const Configuration & _config )

returns true if _config is an endpoint of any existing diff_trans_config

◆ is_primitive()

bool CASM::is_primitive ( const Configuration & _config )

returns true if _config describes primitive cell of the configuration it describes

Definition at line 1045 of file Configuration.cc.

◆ lattice_deformation()

double CASM::lattice_deformation ( const Configuration & _config )

Cost function that describes the degree to which lattice has relaxed.

Definition at line 940 of file Configuration.cc.

◆ make_configuration()

Configuration CASM::make_configuration	(	const PrimClex &	primclex,
		std::string	name
	)

Make Configuration from name string.

For configurations in supercells equivalent to the canonical supercell: For canonical configurations:

CANON_CONFIG_NAME = $CANON_SCELNAME/$CONFIG_INDEX
The CANON_CONFIG is found in the config database by name. For non-canonical configurations:
NONCANON_CONFIG_NAME = $CANON_CONFIG_NAME.equiv.$FG_PERM.$TRANS_PERM
The CANON_CONFIG is found in the config database, then the FG_PERM-th factor_group permutation is applied, follwed by TRANS_PERM-th translation permutation. For all other configurations:
NONEQUIV_SCEL_CONFIG_NAME = $SCEL_NAME/super.$PRIM_FG_OP2.$NONCANON_CONFIG_NAME`
SCEL_NAME may be for a canonical equivalent or non canonical equivalent supercell, in which case it is represented by CANON_SCEL_NAME.$PRIM_FG_OP1
The NONCANON_CONFIG is constructed, PRIM_FG_OP2 is applied, and then the SCEL is filled

Definition at line 783 of file Configuration.cc.

◆ n_species()

double CASM::n_species ( const Configuration & config )

Returns the total number species per unit cell.

Equivalent to

comp_n(config).sum() - n_vacancy(config)

CASM::comp_n

Eigen::VectorXd comp_n(const Configuration &config)

Returns the composition, as number of each species per unit cell.

Definition: Configuration.cc:837

CASM::n_vacancy

double n_vacancy(const Configuration &config)

Returns the vacancy composition, as number per unit cell.

Definition: Configuration.cc:842

CASM::ConfigIO::config

ConfigIO::GenericConfigFormatter< jsonParser > config()

Definition: ConfigIO.cc:777

Definition at line 852 of file Configuration.cc.

◆ n_vacancy()

double CASM::n_vacancy ( const Configuration & config )

Returns the vacancy composition, as number per unit cell.

Definition at line 842 of file Configuration.cc.

◆ num_each_molecule()

Eigen::VectorXi CASM::num_each_molecule	(	const ConfigDoF &	configdof,
		const Supercell &	scel
	)

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

Returns num_each_molecule(molecule_type), where 'molecule_type' is ordered as Structure::xtal::struc_molecule_name()

Definition at line 1282 of file Configuration.cc.

◆ point_corr() [1/2]

Eigen::VectorXd CASM::point_corr	(	Index	linear_unitcell_index,
		Index	neighbor_index,
		const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator const &	clexulator
	)

Returns point correlations from a single site, normalized by cluster orbit size.

Definition at line 1169 of file Configuration.cc.

◆ point_corr() [2/2]

Eigen::VectorXd CASM::point_corr	(	Index	linear_unitcell_index,
		Index	neighbor_index,
		const Configuration &	config,
		Clexulator const &	clexulator
	)

Returns point correlations from a single site, normalized by cluster orbit size.

Definition at line 816 of file Configuration.cc.

◆ reference_energy()

double CASM::reference_energy ( const Configuration & config )

Returns the reference energy, normalized per unit cell.

Definition at line 886 of file Configuration.cc.

◆ reference_energy_per_species()

double CASM::reference_energy_per_species ( const Configuration & config )

Returns the reference energy, normalized per species.

Currently, this is per Molecule

Definition at line 893 of file Configuration.cc.

◆ relaxed_forces()

Eigen::MatrixXd CASM::relaxed_forces ( const Configuration & _config )

relaxed forces of configuration, determined from DFT (eV/Angstr.), as a 3xN matrix

Definition at line 963 of file Configuration.cc.

◆ relaxed_magmom()

double CASM::relaxed_magmom ( const Configuration & _config )

Returns the relaxed magnetic moment, normalized per unit cell.

Definition at line 952 of file Configuration.cc.

◆ relaxed_magmom_per_species()

double CASM::relaxed_magmom_per_species ( const Configuration & _config )

Returns the relaxed magnetic moment, normalized per species.

Definition at line 957 of file Configuration.cc.

◆ rms_force()

double CASM::rms_force ( const Configuration & _config )

Root-mean-square forces of relaxed configurations, determined from DFT (eV/Angstr.)

Definition at line 969 of file Configuration.cc.

◆ site_frac()

Eigen::VectorXd CASM::site_frac ( const Configuration & config )

Returns the composition as site fraction, in the order of Structure::get_struc_molecule.

Returns the composition as site fraction, in the order of Structure::struc_molecule.

Definition at line 870 of file Configuration.cc.

◆ species_frac()

Eigen::VectorXd CASM::species_frac ( const Configuration & config )

Returns the composition as species fraction, with [Va] = 0.0, in the order of Structure::get_struc_molecule.

Returns the composition as species fraction, with [Va] = 0.0, in the order of Structure::struc_molecule.

Currently, this is really a Molecule fraction

Definition at line 860 of file Configuration.cc.

◆ sub_configuration()

Configuration CASM::sub_configuration	(	std::shared_ptr< Supercell const >	sub_scel_ptr,
		const Configuration &	super_config,
		const UnitCell &	origin = `UnitCell(0, 0, 0)`
	)

Returns the sub-configuration that fills a particular Supercell.

Parameters

sub_scel_ptr	The Supercell of the sub-configuration
super_config	The super-configuration
origin	The UnitCell indicating the which unit cell in the super-configuration is the origin in sub-configuration

Copies DoF from the super-configuration directly into the sub-configuration

Definition at line 600 of file Configuration.cc.

◆ volume_relaxation()

double CASM::volume_relaxation ( const Configuration & _config )

Change in volume due to relaxation, expressed as the ratio V/V_0.

Definition at line 945 of file Configuration.cc.

Detailed Description

Modules

Classes

Typedefs

Functions

Typedef Documentation

◆ ConfigurationBase

Function Documentation

◆ atomic_deformation()

◆ clex_formation_energy()

◆ clex_formation_energy_per_species()

◆ closest_setting()

◆ comp()

◆ comp_n() [1/2]

◆ comp_n() [2/2]

◆ config_clip()

◆ config_diff()

◆ corr_contribution() [1/2]

◆ corr_contribution() [2/2]

◆ correlations() [1/2]

◆ correlations() [2/2]

◆ diff_trans_endpoint_of()

◆ energy()

◆ energy_per_species()

◆ formation_energy()

◆ formation_energy_per_species()

◆ gradcorrelations() [1/2]

◆ gradcorrelations() [2/2]

◆ has_atomic_deformation()

◆ has_energy()

◆ has_formation_energy()

◆ has_lattice_deformation()

◆ has_reference_energy()

◆ has_relaxed_mag_basis()

◆ has_relaxed_magmom()

◆ has_rms_force()

◆ has_volume_relaxation()

◆ is_canonical()

◆ is_diff_trans_endpoint()

◆ is_primitive()

◆ lattice_deformation()

◆ make_configuration()

◆ n_species()

◆ n_vacancy()

◆ num_each_molecule()

◆ point_corr() [1/2]

◆ point_corr() [2/2]

◆ reference_energy()

◆ reference_energy_per_species()

◆ relaxed_forces()

◆ relaxed_magmom()

◆ relaxed_magmom_per_species()

◆ rms_force()

◆ site_frac()

◆ species_frac()

◆ sub_configuration()

◆ volume_relaxation()