Detailed Description

PrimClex is the top-level data structure for a CASM project.

Classes
class	CASM::DB::ValDatabase< ValueType >
	Generic interface for database of a particular CASM type. More...

class	CASM::DB::Database< T >

class	CASM::PrimClex
	PrimClex is the top-level data structure for a CASM project. More...

Typedefs
typedef Structure	CASM::PrimClex::PrimType

Functions
	CASM::PrimClex::PrimClex (ProjectSettings const &_project_settings, std::shared_ptr< PrimType const > _shared_prim)
	Initial construction of a PrimClex, from ProjectSettings and shared prim. More...

	CASM::PrimClex::PrimClex (const fs::path &_root)

	CASM::PrimClex::PrimClex (const PrimClex &)=delete

	CASM::PrimClex::~PrimClex ()
	Necessary for "pointer to implementation". More...

void	CASM::PrimClex::refresh (bool read_settings=false, bool read_composition=false, bool read_chem_ref=false, bool read_configs=false, bool clear_clex=false)
	Reload PrimClex data from settings. More...

ProjectSettings &	CASM::PrimClex::settings ()

const ProjectSettings &	CASM::PrimClex::settings () const

bool	CASM::PrimClex::has_dir () const
	Check if DirectoryStructure exists. More...

const DirectoryStructure &	CASM::PrimClex::dir () const
	Access DirectoryStructure object. Throw if not set. More...

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

bool	CASM::PrimClex::has_composition_axes () const
	check if CompositionConverter object initialized More...

const CompositionConverter &	CASM::PrimClex::composition_axes () const
	const Access CompositionConverter object More...

bool	CASM::PrimClex::has_chemical_reference () const
	check if ChemicalReference object initialized More...

const ChemicalReference &	CASM::PrimClex::chemical_reference () const
	const Access ChemicalReference object More...

const PrimType &	CASM::PrimClex::prim () const
	const Access to primitive Structure More...

std::shared_ptr< PrimType const > const &	CASM::PrimClex::shared_prim () const
	Access to the primitive Structure as a shared resource. More...

Index	CASM::PrimClex::n_basis () const
	const Access to number of basis atoms More...

std::shared_ptr< PrimNeighborList > const &	CASM::PrimClex::shared_nlist () const
	Access to the primitive neighbor list as a shared resource. More...

PrimNeighborList &	CASM::PrimClex::nlist () const
	Access to the primitive neighbor list. More...

bool	CASM::PrimClex::vacancy_allowed () const
	returns true if vacancy are an allowed species More...

Index	CASM::PrimClex::vacancy_index () const
	returns the index of vacancies in composition vectors More...

template<typename T >
DB::ValDatabase< T > &	CASM::PrimClex::generic_db () const

template<typename T >
const DB::ValDatabase< T > &	CASM::PrimClex::const_generic_db () const

template<typename T >
DB::Database< T > &	CASM::PrimClex::db () const

template<typename T >
const DB::Database< T > &	CASM::PrimClex::const_db () const

template<typename T >
DB::PropertiesDatabase &	CASM::PrimClex::db_props (std::string calc_type) const

template<typename T >
const DB::PropertiesDatabase &	CASM::PrimClex::const_db_props (std::string calc_type) const

DB::DatabaseHandler &	CASM::PrimClex::db_handler () const

const DB::DatabaseHandler &	CASM::PrimClex::const_db_handler () const

bool	CASM::PrimClex::has_basis_set_specs (std::string const &basis_set_name) const

ClexBasisSpecs const &	CASM::PrimClex::basis_set_specs (std::string const &basis_set_name) const

Clexulator	CASM::PrimClex::clexulator (std::string const &basis_set_name) const

bool	CASM::PrimClex::has_eci (const ClexDescription &key) const

ECIContainer const &	CASM::PrimClex::eci (const ClexDescription &key) const

void	CASM::PrimClex::_init ()
	Initialization routines. More...

void	CASM::write_basis_set_data (std::shared_ptr< Structure const > shared_prim, ProjectSettings const &settings, std::string const &basis_set_name, ClexBasisSpecs const &basis_set_specs, PrimNeighborList &prim_neighbor_list)

Clexulator	CASM::make_clexulator (ProjectSettings const &settings, std::string const &basis_set_name, PrimNeighborList &prim_neighbor_list)

Variables
std::unique_ptr< PrimClexData >	CASM::PrimClex::m_data

Typedef Documentation

◆ PrimType

typedef Structure CASM::PrimClex::PrimType

Definition at line 57 of file PrimClex.hh.

Function Documentation

◆ _init()

void CASM::PrimClex::_init ( )

private

Initialization routines.

Initialization routines

If !root.empty(), read all saved data to generate all Supercells and Configurations, etc.

Definition at line 121 of file PrimClex.cc.

◆ basis_set_specs()

ClexBasisSpecs const & CASM::PrimClex::basis_set_specs ( std::string const & basis_set_name ) const

Definition at line 344 of file PrimClex.cc.

◆ chemical_reference()

const ChemicalReference & CASM::PrimClex::chemical_reference ( ) const

const Access ChemicalReference object

Definition at line 255 of file PrimClex.cc.

◆ clexulator()

Clexulator CASM::PrimClex::clexulator ( std::string const & basis_set_name ) const

Definition at line 366 of file PrimClex.cc.

◆ composition_axes()

const CompositionConverter & CASM::PrimClex::composition_axes ( ) const

const Access CompositionConverter object

Definition at line 243 of file PrimClex.cc.

◆ const_db()

template<typename T >

const DB::Database< T > & CASM::PrimClex::const_db

Definition at line 307 of file PrimClex.cc.

◆ const_db_handler()

const DB::DatabaseHandler & CASM::PrimClex::const_db_handler ( ) const

Definition at line 329 of file PrimClex.cc.

◆ const_db_props()

template<typename T >

const DB::PropertiesDatabase & CASM::PrimClex::const_db_props ( std::string calc_type ) const

Definition at line 317 of file PrimClex.cc.

◆ const_generic_db()

template<typename T >

const DB::ValDatabase< T > & CASM::PrimClex::const_generic_db

Definition at line 297 of file PrimClex.cc.

◆ crystallography_tol()

double CASM::PrimClex::crystallography_tol ( ) const

Get the crystallography_tol.

Definition at line 233 of file PrimClex.cc.

◆ db()

template<typename T >

DB::Database< T > & CASM::PrimClex::db

Definition at line 302 of file PrimClex.cc.

◆ db_handler()

DB::DatabaseHandler & CASM::PrimClex::db_handler ( ) const

Definition at line 322 of file PrimClex.cc.

◆ db_props()

template<typename T >

DB::PropertiesDatabase & CASM::PrimClex::db_props ( std::string calc_type ) const

Definition at line 312 of file PrimClex.cc.

◆ dir()

const DirectoryStructure & CASM::PrimClex::dir ( ) const

Access DirectoryStructure object. Throw if not set.

Definition at line 230 of file PrimClex.cc.

◆ eci()

const ECIContainer & CASM::PrimClex::eci ( const ClexDescription & key ) const

Definition at line 406 of file PrimClex.cc.

◆ generic_db()

template<typename T >

DB::ValDatabase< T > & CASM::PrimClex::generic_db

Definition at line 292 of file PrimClex.cc.

◆ has_basis_set_specs()

bool CASM::PrimClex::has_basis_set_specs ( std::string const & basis_set_name ) const

Definition at line 336 of file PrimClex.cc.

◆ has_chemical_reference()

bool CASM::PrimClex::has_chemical_reference ( ) const

check if ChemicalReference object initialized

Definition at line 250 of file PrimClex.cc.

◆ has_composition_axes()

bool CASM::PrimClex::has_composition_axes ( ) const

check if CompositionConverter object initialized

const Access CompositionConverter object

Definition at line 238 of file PrimClex.cc.

◆ has_dir()

bool CASM::PrimClex::has_dir ( ) const

Check if DirectoryStructure exists.

Definition at line 228 of file PrimClex.cc.

◆ has_eci()

bool CASM::PrimClex::has_eci ( const ClexDescription & key ) const

Definition at line 397 of file PrimClex.cc.

◆ make_clexulator()

Clexulator CASM::make_clexulator	(	ProjectSettings const &	settings,
		std::string const &	basis_set_name,
		PrimNeighborList &	prim_neighbor_list
	)

Make Clexulator from existing source code

Notes:

Use write_basis_set_data to write Clexulator source code prior to calling this function.
This function will compile the Clexulator source code if that has not yet been done.

Definition at line 524 of file PrimClex.cc.

◆ n_basis()

Index CASM::PrimClex::n_basis ( ) const

const Access to number of basis atoms

Definition at line 268 of file PrimClex.cc.

◆ nlist()

PrimNeighborList & CASM::PrimClex::nlist ( ) const

Access to the primitive neighbor list.

Definition at line 283 of file PrimClex.cc.

◆ prim()

const PrimClex::PrimType & CASM::PrimClex::prim ( ) const

const Access to primitive Structure

Definition at line 262 of file PrimClex.cc.

◆ PrimClex() [1/3]

CASM::PrimClex::PrimClex ( const fs::path & _root )

explicit

Construct PrimClex from existing CASM project directory

read PrimClex and directory structure to generate all its Supercells and Configurations, etc.

Definition at line 111 of file PrimClex.cc.

◆ PrimClex() [2/3]

CASM::PrimClex::PrimClex ( const PrimClex & )

delete

◆ PrimClex() [3/3]

CASM::PrimClex::PrimClex	(	ProjectSettings const &	_project_settings,
		std::shared_ptr< PrimType const >	_shared_prim
	)

explicit

Initial construction of a PrimClex, from ProjectSettings and shared prim.

Initial construction of a PrimClex, from a primitive Structure.

Definition at line 98 of file PrimClex.cc.

◆ refresh()

void CASM::PrimClex::refresh	(	bool	read_settings = `false`,
		bool	read_composition = `false`,
		bool	read_chem_ref = `false`,
		bool	read_configs = `false`,
		bool	clear_clex = `false`
	)

Reload PrimClex data from settings.

Parameters

read_settings	Read project_settings.json and plugins
read_composition	Read composition_axes.json
read_chem_ref	Read chemical_reference.json
read_configs	Read SCEL and config_list.json
clear_clex	Clear stored orbitrees, clexulators, and eci

This does not check if what you request will cause problems.
ToDo: refactor into separate functions

Definition at line 156 of file PrimClex.cc.

◆ settings() [1/2]

ProjectSettings & CASM::PrimClex::settings ( )

Definition at line 224 of file PrimClex.cc.

◆ settings() [2/2]

const ProjectSettings & CASM::PrimClex::settings ( ) const

Definition at line 226 of file PrimClex.cc.

◆ shared_nlist()

std::shared_ptr< PrimNeighborList > const & CASM::PrimClex::shared_nlist ( ) const

Access to the primitive neighbor list as a shared resource.

Definition at line 270 of file PrimClex.cc.

◆ shared_prim()

std::shared_ptr< PrimClex::PrimType const > const & CASM::PrimClex::shared_prim ( ) const

Access to the primitive Structure as a shared resource.

Definition at line 264 of file PrimClex.cc.

◆ vacancy_allowed()

bool CASM::PrimClex::vacancy_allowed ( ) const

returns true if vacancy are an allowed species

Definition at line 286 of file PrimClex.cc.

◆ vacancy_index()

Index CASM::PrimClex::vacancy_index ( ) const

returns the index of vacancies in composition vectors

Definition at line 289 of file PrimClex.cc.

◆ write_basis_set_data()

void CASM::write_basis_set_data	(	std::shared_ptr< Structure const >	shared_prim,
		ProjectSettings const &	settings,
		std::string const &	basis_set_name,
		ClexBasisSpecs const &	basis_set_specs,
		PrimNeighborList &	prim_neighbor_list
	)

Write clust.json, basis.json, and clexulator source code, by constructing orbits and ClexBasis

Notes:

Overwrites any existing files
Uses DoFType::traits_dict() for DoFTraits

Write clexulator, clust.json, basis.json by constructing orbits and ClexBasis

Definition at line 504 of file PrimClex.cc.

◆ ~PrimClex()

CASM::PrimClex::~PrimClex ( )

Necessary for "pointer to implementation".

Definition at line 116 of file PrimClex.cc.

Variable Documentation

◆ m_data

std::unique_ptr<PrimClexData> CASM::PrimClex::m_data

private

Definition at line 175 of file PrimClex.hh.

Detailed Description

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ PrimType

Function Documentation

◆ _init()

◆ basis_set_specs()

◆ chemical_reference()

◆ clexulator()

◆ composition_axes()

◆ const_db()

◆ const_db_handler()

◆ const_db_props()

◆ const_generic_db()

◆ crystallography_tol()

◆ db()

◆ db_handler()

◆ db_props()

◆ dir()

◆ eci()

◆ generic_db()

◆ has_basis_set_specs()

◆ has_chemical_reference()

◆ has_composition_axes()

◆ has_dir()

◆ has_eci()

◆ make_clexulator()

◆ n_basis()

◆ nlist()

◆ prim()

◆ PrimClex() [1/3]

◆ PrimClex() [2/3]

◆ PrimClex() [3/3]

◆ refresh()

◆ settings() [1/2]

◆ settings() [2/2]

◆ shared_nlist()

◆ shared_prim()

◆ vacancy_allowed()

◆ vacancy_index()

◆ write_basis_set_data()

◆ ~PrimClex()

Variable Documentation

◆ m_data