#include <Structure.hh>

Inheritance diagram for CASM::Structure:

Detailed Description

Structure specifies the lattice and atomic basis of a crystal.

Definition at line 29 of file Structure.hh.

Public Member Functions
	Structure ()

	Structure (const Lattice &init_lat)

	Structure (const BasicStructure< Site > &base)

	Structure (const fs::path &filepath)

	Structure (const Structure &RHS)

const MasterSymGroup &	factor_group () const

const SymGroup &	point_group () const

SymGroupRep const *	basis_permutation_symrep () const

SymGroupRepID	basis_permutation_symrep_ID () const

std::vector< Specie >	get_struc_specie () const
	Returns an Array of each possible Specie in this Structure. More...

std::vector< Molecule >	get_struc_molecule () const
	Returns an Array of each possible Molecule in this Structure. More...

std::vector< std::string >	get_struc_molecule_name () const
	Returns an Array of each possible Molecule in this Structure. More...

Eigen::VectorXi	get_num_each_specie () const

Eigen::VectorXi	get_num_each_molecule () const

Structure &	operator= (const Structure &RHS)

void	copy_attributes_from (const Structure &RHS)
	copy all non-derived members More...

void	reset ()
	clears symmetry, site internals, and other attributes More...

void	set_lattice (const Lattice &lattice, COORD_TYPE mode)

void	generate_factor_group (double map_tol=TOL) const

void	generate_factor_group_slow (double map_tol=TOL) const
	Obtain factor group by testing all operations of the lattice point_group and keep. More...

void	fg_converge (double large_tol)
	generate factor groups for a range of tol values, prints results to screen (for now) More...

void	fg_converge (double small_tol, double large_tol, double increment)

SymGroupRepID	generate_basis_permutation_representation (bool verbose=false) const
	Obtain the basis permutation representation of factor_group, returns its rep_id, and sets internal basis_perm_rep_ID. More...

void	symmetrize (const SymGroup &relaxed_factors)

void	symmetrize (const double &tolerace)

void	fill_supercell (const Structure &prim, double map_tol=TOL)
	fill an empty structure with the basis of its corresponding primitive cell - performs optimized factor_group expansion More...

Structure	create_superstruc (const Lattice &scel_lat, double map_tol=TOL) const
	Shortcut routine to create a supercell structure and fill it with sites. More...

void	map_superstruc_to_prim (Structure &prim)
	Figures out which prim basis each superstructure basis corresponds to. More...

void	set_occs (Array< int > occ_index)
	Setting the current occupants of the structure to those specified by an array of integers. More...

void	generate_basis_bouquet (const SiteOrbitree &in_tree, SiteOrbitree &out_tree, Index num_sites, double tol)

void	generate_asym_bouquet (const SiteOrbitree &in_tree, SiteOrbitree &out_tree, Index num_sites, double tol)

void	generate_flowertrees_safe (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees, double tol=TOL)
	Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed. More...

void	generate_flowertrees (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees, double tol=TOL)

Structure	stack_on (const Structure &understruc, bool override=0) const

Structure	get_reflection () const
	Return reflection of structure. More...

void	clump_atoms (double maxdist, double tol)
	If atoms are too close together, average their distance and make them one. More...

void	sort_basis ()
	Rearrange basis by grouping atoms by type. More...

Structure	stamp_with (SiteCluster stamp, bool lat_override=0, bool im_override=0) const

Array< Structure >	bedazzle (Array< SiteCluster > stamps, bool lat_override=0, bool im_override=0) const

Array< Array< Array< double > > >	get_NN_table (const double &maxr, SiteOrbitree &bouquet, double tol)

Array< Array< Array< double > > >	get_NN_table (const double &maxr, double tol)

void	add_vacuum_shift (Structure &new_surface_struc, double vacuum_thickness, Eigen::Vector3d shift, COORD_TYPE mode) const
	Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0) More...

void	add_vacuum_shift (Structure &new_surface_struc, double vacuum_thickness, Coordinate shift) const

void	add_vacuum (Structure &new_surface_struc, double vacuum_thickness) const
	Adds vacuum layer on top of ab plane. More...

Structure &	operator+= (const Coordinate &shift)
	Translates all atoms in cell. More...

Structure &	operator-= (const Coordinate &shift)

void	intpol (Structure end_struc, int Nofimag, PERIODICITY_TYPE mode, Array< Structure > &images)

void	print_site_symmetry (std::ostream &stream, COORD_TYPE mode, int shorttag, double tol)
	For each symmetrically distinct site, print the symmetry operations that map it onto itself. More...

bool	read_species ()

void	assign_species (Array< std::string > &names, Array< double > &masses, Array< double > &magmoms, Array< double > &Us, Array< double > &Js)

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

Index	find (const CoordType2 &test_site, double tol=TOL) const

Index	find (const CoordType2 &test_site, const Coordinate &shift, double tol) const

const Lattice &	lattice () const

UnitCellCoord	get_unit_cell_coord (const CoordType2 &test_site, double tol=TOL) const

void	copy_attributes_from (const BasicStructure &RHS)

void	update ()

void	set_site_internals ()
	Associate each site with its basis index by setting its internal flags (asym_ind -> -1) More...

void	within ()
	Translate all basis sites so that they are inside the unit cell. More...

Site	get_site (const UnitCellCoord &ucc) const

void	set_basis (Array< Site > basis_in)
	Manually set the basis sites. More...

void	generate_factor_group (SymGroup &factor_group, double map_tol) const
	apply a symmetry operation to the current structure (may change lattice vectors and order of basis atoms) More...

void	generate_factor_group_slow (SymGroup &factor_group, double map_tol) const

void	fg_converge (SymGroup &factor_group, double small_tol, double large_tol, double increment)

SymGroupRepID	generate_basis_permutation_representation (const MasterSymGroup &factor_group, bool verbose) const

bool	is_primitive (double prim_tol=TOL) const

bool	is_primitive (BasicStructure &new_prim, double prim_tol=TOL) const

void	fill_supercell (const BasicStructure &prim, double map_tol=TOL)
	fill an empty structure with the basis of its corresponding primitive cell More...

void	generate_flowertrees_safe (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees)
	Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed. More...

void	generate_flowertrees (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees)

void	map_superstruc_to_prim (BasicStructure &prim, const SymGroup &point_group)
	Figures out which prim basis each superstructure basis corresponds to. More...

void	merge_sites (double maxdist)
	If atoms are too close together, average their distance and make them one. More...

void	add_vacuum_shift (BasicStructure &new_surface_struc, double vacuum_thickness, Eigen::Vector3d shift, COORD_TYPE mode) const
	Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0) More...

void	add_vacuum_shift (BasicStructure &new_surface_struc, double vacuum_thickness, Coordinate shift) const

void	add_vacuum (BasicStructure &new_surface_struc, double vacuum_thickness) const
	Adds vacuum layer on top of ab plane. More...

Index	max_possible_vacancies () const
	Counts sites that allow vacancies. More...

const Lattice &	get_lattice () const
	Return a reference to the lattice. More...

virtual void	read (std::istream &stream)
	Print intpolated images in seperate directries. More...

void	print_xyz (std::ostream &stream) const
	Output other formats. More...

void	print_cif (std::ostream &stream) const

Public Attributes
std::string	title
	User-specified name of this Structure. More...

Array< Site >	basis
	Lattice vectors that specifies periodicity of the crystal. More...

Protected Attributes
MasterSymGroup	m_factor_group

SymGroupRepID	basis_perm_rep_ID
	This holds the representation id of the permutation representation. More...

bool	SD_flag
	Specifies whether selectice dynamics is on or of for DFT calculations. More...

Lattice	m_lattice

Private Member Functions
void	main_print (std::ostream &stream, COORD_TYPE mode, bool version5, int option) const
	*** Inherited from BasicStructure<Site> More...

Constructor & Destructor Documentation

CASM::Structure::Structure ( )

inline

Definition at line 57 of file Structure.hh.

CASM::Structure::Structure ( const Lattice & init_lat )

inlineexplicit

Definition at line 58 of file Structure.hh.

CASM::Structure::Structure ( const BasicStructure< Site > & base )

inlineexplicit

Definition at line 59 of file Structure.hh.

CASM::Structure::Structure ( const fs::path & filepath )

explicit

Definition at line 18 of file Structure.cc.

CASM::Structure::Structure ( const Structure & RHS )

Have to explicitly define the copy constructor so that factor_group does not depend on the lattice of 'RHS'

Definition at line 31 of file Structure.cc.

Member Function Documentation

void CASM::BasicStructure< Site >::add_vacuum	(	BasicStructure< Site > &	new_surface_struc,
		double	vacuum_thickness
	)		const

inherited

Adds vacuum layer on top of ab plane.

void CASM::Structure::add_vacuum	(	Structure &	new_surface_struc,
		double	vacuum_thickness
	)		const

Adds vacuum layer on top of ab plane.

Definition at line 1117 of file Structure.cc.

void CASM::BasicStructure< Site >::add_vacuum_shift	(	BasicStructure< Site > &	new_surface_struc,
		double	vacuum_thickness,
		Eigen::Vector3d	shift,
		COORD_TYPE	mode
	)		const

inherited

Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0)

Call this on a structure to get new_surface_struc: the structure with a layer of vacuum added parallel to the ab plane. vacuum_thickness: thickness of vacuum layer (Angstroms) shift: shift vector from layer to layer, assumes FRAC unless specified. The shift vector should only have values relative to a and b vectors (eg x, y, 0). Default shift is zero.

void CASM::BasicStructure< Site >::add_vacuum_shift	(	BasicStructure< Site > &	new_surface_struc,
		double	vacuum_thickness,
		Coordinate	shift
	)		const

inherited

void CASM::Structure::add_vacuum_shift	(	Structure &	new_surface_struc,
		double	vacuum_thickness,
		Eigen::Vector3d	shift,
		COORD_TYPE	mode
	)		const

Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0)

Call this on a structure to get new_surface_struc: the structure with a layer of vacuum added parallel to the ab plane. vacuum_thickness: thickness of vacuum layer (Angstroms) shift: shift vector from layer to layer, assumes FRAC unless specified. The shift vector should only have values relative to a and b vectors (eg x, y, 0). Default shift is zero.

Definition at line 1088 of file Structure.cc.

void CASM::Structure::add_vacuum_shift	(	Structure &	new_surface_struc,
		double	vacuum_thickness,
		Coordinate	shift
	)		const

Definition at line 1110 of file Structure.cc.

void CASM::Structure::assign_species	(	Array< std::string > &	names,
		Array< double > &	masses,
		Array< double > &	magmoms,
		Array< double > &	Us,
		Array< double > &	Js
	)

SymGroupRep const * CASM::Structure::basis_permutation_symrep ( ) const

Definition at line 107 of file Structure.cc.

SymGroupRepID CASM::Structure::basis_permutation_symrep_ID ( ) const

Definition at line 113 of file Structure.cc.

Array< Structure > CASM::Structure::bedazzle	(	Array< SiteCluster >	stamps,
		bool	lat_override = `0`,
		bool	im_override = `0`
	)		const

Same as stamp_with, but takes an array of clusters and returns and array of structures. Basically saves you a for loop. Perhaps this should actually take an OrbitBranch?

Definition at line 945 of file Structure.cc.

void CASM::Structure::clump_atoms	(	double	mindist,
		double	tol
	)

If atoms are too close together, average their distance and make them one.

Given a minimum distance, find pair clusters within this length and average out the distance between the two atoms and put one atom there, eliminating the other two. Meant to be used for grain boundaries.

This function is meant for averaging atoms of the same type!

Definition at line 793 of file Structure.cc.

void CASM::Structure::copy_attributes_from ( const Structure & RHS )

copy all non-derived members

Definition at line 62 of file Structure.cc.

void CASM::BasicStructure< Site >::copy_attributes_from ( const BasicStructure< Site > & RHS )

inherited

Use this is the copy interface for things that derive from BasicStructure<> It should be overloaded in derived classes so that all important attributes besides lattice, basis, and title get copied

Structure CASM::Structure::create_superstruc	(	const Lattice &	scel_lat,
		double	map_tol = `TOL`
	)		const

Shortcut routine to create a supercell structure and fill it with sites.

Operates on the primitive structure and takes as an argument the supercell lattice. It then returns a new superstructure.

This is similar to the Lattice*Primitive routine which returns a new superstructure. Unlike the fill_supercell routine which takes the primitive structure, this WILL fill the sites.

Definition at line 335 of file Structure.cc.

const MasterSymGroup & CASM::Structure::factor_group ( ) const

Definition at line 94 of file Structure.cc.

void CASM::Structure::fg_converge ( double large_tol )

generate factor groups for a range of tol values, prints results to screen (for now)

Definition at line 231 of file Structure.cc.

void CASM::Structure::fg_converge	(	double	small_tol,
		double	large_tol,
		double	increment
	)

Definition at line 225 of file Structure.cc.

void CASM::BasicStructure< Site >::fg_converge	(	SymGroup &	factor_group,
		double	small_tol,
		double	large_tol,
		double	increment
	)

inherited

void CASM::Structure::fill_supercell	(	const Structure &	prim,
		double	map_tol = `TOL`
	)

fill an empty structure with the basis of its corresponding primitive cell - performs optimized factor_group expansion

Returns true if the structure describes a crystal primitive cell i.e., no translation smaller than a lattice vector can map the structure onto itself Returns true if the structure describes a crystal primitive cell and finds the primitive cell and stores it in 'new_prim'

It is NOT wise to use this function unless you have already initialized a superstructure with lattice vectors.

It is more wise to use the two methods that call this method: Either the overloaded * operator which does: SCEL_Lattice * Prim_Structrue = New_Superstructure — or — New_Superstructure=Prim_Structure.create_superstruc(SCEL_Lattice);

Both of these will return NEW superstructures.

Definition at line 263 of file Structure.cc.

void CASM::BasicStructure< Site >::fill_supercell	(	const BasicStructure< Site > &	prim,
		double	map_tol = `TOL`
	)

inherited

fill an empty structure with the basis of its corresponding primitive cell

It is NOT wise to use this function unless you have already initialized a superstructure with lattice vectors.

It is more wise to use the two methods that call this method: Either the overloaded * operator which does: SCEL_Lattice * Prim_Structrue = New_Superstructure — or — New_Superstructure=Prim_BasicStructure<CoordType>.create_superstruc(SCEL_Lattice);

Both of these will return NEW superstructures.

Index CASM::BasicStructure< Site >::find	(	const CoordType2 &	test_site,
		double	tol = `TOL`
	)		const

inherited

return basis index of site that matches test_coord, if it is in basis otherwise, returns basis.size()

Index CASM::BasicStructure< Site >::find	(	const CoordType2 &	test_site,
		const Coordinate &	shift,
		double	tol
	)		const

inherited

return basis index of site that matches test_site+shift, if it is in basis otherwise, returns basis.size()

void CASM::Structure::from_json ( const jsonParser & json )

re-throw exceptions

Definition at line 1241 of file Structure.cc.

void CASM::Structure::generate_asym_bouquet	(	const SiteOrbitree &	in_tree,
		SiteOrbitree &	out_tree,
		Index	num_sites,
		double	tol
	)

For each asymmetric unit site, find each cluster in 'in_tree' that contain that basis site, create an orbit of all equivalent clusters that also contain the basis site and store each of these orbits in out_tree num_sites specifies what size of clusters are desired (e.g., pairs, triplets, etc)

Fills out_tree with OrbitBranches with pivots corresponding to the different asym_unit sites. The orbits of each branch are "petals" radiating from that branch's pivot.

Parameters

in_tree	General tree that holds clusters of all sizes
out_tree	Holds all flowers (orbits) radiating from asym_unit sites
num_sites	Size of clusters filling up out_tree

Definition at line 501 of file Structure.cc.

void CASM::Structure::generate_basis_bouquet	(	const SiteOrbitree &	in_tree,
		SiteOrbitree &	out_tree,
		Index	num_sites,
		double	tol
	)

For each basis site, find each cluster in 'in_tree' that contain that basis site, create an orbit of all equivalent clusters that also contain the basis site and store each of these orbits in out_tree num_sites specifies what size of clusters are desired (e.g., pairs, triplets, etc)

Definition at line 446 of file Structure.cc.

SymGroupRepID CASM::Structure::generate_basis_permutation_representation ( bool verbose = false ) const

Obtain the basis permutation representation of factor_group, returns its rep_id, and sets internal basis_perm_rep_ID.

Definition at line 1182 of file Structure.cc.

SymGroupRepID CASM::BasicStructure< Site >::generate_basis_permutation_representation	(	const MasterSymGroup &	factor_group,
		bool	verbose
	)		const

inherited

void CASM::Structure::generate_factor_group ( double map_tol = TOL ) const

apply a symmetry operation to the current structure (does not change lattice vectors, because 'op' is assumed to be a lattice homomorphism) determines primitive cell, finds its factor group using generate_factor_group_slow, and then expands the factor group into the supercell using lattice translations

Definition at line 85 of file Structure.cc.

void CASM::BasicStructure< Site >::generate_factor_group	(	SymGroup &	factor_group,
		double	map_tol
	)		const

inherited

apply a symmetry operation to the current structure (may change lattice vectors and order of basis atoms)

void CASM::Structure::generate_factor_group_slow ( double map_tol = TOL ) const

Obtain factor group by testing all operations of the lattice point_group and keep.

Definition at line 77 of file Structure.cc.

void CASM::BasicStructure< Site >::generate_factor_group_slow	(	SymGroup &	factor_group,
		double	map_tol
	)		const

inherited

void CASM::BasicStructure< Site >::generate_flowertrees	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees
	)

inherited

void CASM::Structure::generate_flowertrees	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees,
		double	tol = `TOL`
	)

A flowertree has clusters of every size organized like the branches of a regular orbitree, but every cluster in the entire flowertree has the same pivot.

Definition at line 410 of file Structure.cc.

void CASM::BasicStructure< Site >::generate_flowertrees_safe	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees
	)

inherited

Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed.

void CASM::Structure::generate_flowertrees_safe	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees,
		double	tol = `TOL`
	)

Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed.

A flowertree is NOT a bouquet. Bouquets are constructed from an orbitree (generate_basis_bouquet) by taking every cluster of a given size and storing them in branches, where each branch contains clusters with a common pivot. A flowertree has clusters of every size organized like the branches of a regular orbitree, but every cluster in the entire flowertree has the same pivot.

Begin by making n bouquets, where n is the size of the larges cluster in the provided orbitree. Then shuffle all the bouquets together and sort them by basis site. The result is an array of "flowertrees", which have been made by picking out flowers of every bouquet that have the same pivot. You end up with one flowertree per basis site each of which has clusters from size 1 to n.

Definition at line 562 of file Structure.cc.

const Lattice& CASM::BasicStructure< Site >::get_lattice ( ) const

inlineinherited

Return a reference to the lattice.

Definition at line 177 of file BasicStructure.hh.

Array< Array< Array< double > > > CASM::Structure::get_NN_table	(	const double &	maxr,
		SiteOrbitree &	bouquet,
		double	tol
	)

Goes to a specified site of the basis and makes a flower tree of pairs. It then stores the length and multiplicity of the pairs in a double array, giving you a strict nearest neighbor table. This version also fills up a SiteOrbitree in case you want to keep it. Blatantly copied from Anna's routine in old new CASM

Definition at line 965 of file Structure.cc.

Array< Array< Array< double > > > CASM::Structure::get_NN_table	(	const double &	maxr,
		double	tol
	)

Goes to a specified site of the basis and makes a flower tree of pairs. It then stores the length and multiplicity of the pairs in a double array, giving you a strict nearest neighbor table. The bouquet used for this falls into the void.

Definition at line 1008 of file Structure.cc.

Eigen::VectorXi CASM::Structure::get_num_each_molecule ( ) const

Returns a list of how many of each molecule exist in this Structure The molecule types are ordered according to get_struc_molecule()

Definition at line 206 of file Structure.cc.

Eigen::VectorXi CASM::Structure::get_num_each_specie ( ) const

Returns a list of how many of each specie exist in this Structure The Specie types are ordered according to get_struc_specie()

Definition at line 184 of file Structure.cc.

Structure CASM::Structure::get_reflection ( ) const

Return reflection of structure.

Makes reflection of structure and returns new reflected strucutre. Meant for primitive structures, but can be forced on superstructures. If forced on non primitive structure then the reflected structure will think it's primitive. To avoid this issue reflect primitive structure and then make a reflected superlattice to fill it with.

Definition at line 769 of file Structure.cc.

Site CASM::BasicStructure< Site >::get_site ( const UnitCellCoord & ucc ) const

inherited

std::vector< Molecule > CASM::Structure::get_struc_molecule ( ) const

Returns an Array of each possible Molecule in this Structure.

Definition at line 146 of file Structure.cc.

std::vector< std::string > CASM::Structure::get_struc_molecule_name ( ) const

Returns an Array of each possible Molecule in this Structure.

Definition at line 166 of file Structure.cc.

std::vector< Specie > CASM::Structure::get_struc_specie ( ) const

Returns an Array of each possible Specie in this Structure.

Definition at line 123 of file Structure.cc.

UnitCellCoord CASM::BasicStructure< Site >::get_unit_cell_coord	(	const CoordType2 &	test_site,
		double	tol = `TOL`
	)		const

inherited

Return the UnitCellCoord corresponding to test_site (i.e., finds the basis index and the lattice translation)

Using the lattice of (*this), this function will return a UnitCellCoord that corresponds to a site passed to it within a given tolerance. This function is useful for making a nearest neighbor table from sites that land outside of the primitive cell.

void CASM::Structure::intpol	(	Structure	end_struc,
		int	Nofimag,
		PERIODICITY_TYPE	mode,
		Array< Structure > &	images
	)

Creates Nofimag POSCAR files by interpolating linearly between structures in star_stru and end_stru for exact interpolation, choose "LOCAL" or "1", for nearest-image interpolation, choose "PERIODIC" or "0"

Creates N of image POSCAR files in seperate directories by interpolating linearly between structures. For exact interpolation, choose " LOCAL " or "1" in mode For nearest-image interpolation, chosse "PERIODIC" or "0"

Stored in Array<Structure> images; images[0] = start structure, images[Nofimage+1] = end structure

Definition at line 1139 of file Structure.cc.

bool CASM::BasicStructure< Site >::is_primitive ( double prim_tol = TOL ) const

inherited

Returns true if the structure describes a crystal primitive cell i.e., no translation smaller than a lattice vector can map the structure onto itself

Determines if structure is primitive description of the crystal

bool CASM::BasicStructure< Site >::is_primitive	(	BasicStructure< Site > &	new_prim,
		double	prim_tol = `TOL`
	)		const

inherited

Returns true if the structure describes a crystal primitive cell and finds the primitive cell and stores it in 'new_prim'

Determines if structure is primitive description of the crystal If not, finds primitive cell and copies to new_prim

const Lattice& CASM::BasicStructure< Site >::lattice ( ) const

inlineinherited

Definition at line 74 of file BasicStructure.hh.

void CASM::Structure::main_print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		bool	version5,
		int	option
	)		const

private

*** Inherited from BasicStructure<Site>

void CASM::Structure::map_superstruc_to_prim ( Structure & prim )

Figures out which prim basis each superstructure basis corresponds to.

Definition at line 605 of file Structure.cc.

void CASM::BasicStructure< Site >::map_superstruc_to_prim	(	BasicStructure< Site > &	prim,
		const SymGroup &	point_group
	)

inherited

Figures out which prim basis each superstructure basis corresponds to.

Index CASM::BasicStructure< Site >::max_possible_vacancies ( ) const

inherited

Counts sites that allow vacancies.

void CASM::BasicStructure< Site >::merge_sites ( double maxdist )

inherited

If atoms are too close together, average their distance and make them one.

Structure & CASM::Structure::operator+= ( const Coordinate & shift )

Translates all atoms in cell.

Definition at line 1201 of file Structure.cc.

Structure & CASM::Structure::operator-= ( const Coordinate & shift )

Definition at line 1213 of file Structure.cc.

Structure & CASM::Structure::operator= ( const Structure & RHS )

Have to explicitly define the assignment operator so that sites in this structure do not depend on the lattice of 'RHS'

Definition at line 40 of file Structure.cc.

const SymGroup & CASM::Structure::point_group ( ) const

Definition at line 101 of file Structure.cc.

void CASM::BasicStructure< Site >::print_cif ( std::ostream & stream ) const

inherited

void CASM::Structure::print_site_symmetry	(	std::ostream &	stream,
		COORD_TYPE	mode,
		int	shorttag = `1`,
		double	tol = `TOL`
	)

For each symmetrically distinct site, print the symmetry operations that map it onto itself.

Definition at line 348 of file Structure.cc.

void CASM::BasicStructure< Site >::print_xyz ( std::ostream & stream ) const

inherited

Output other formats.

virtual void CASM::BasicStructure< Site >::read ( std::istream & stream )

virtualinherited

Print intpolated images in seperate directries.

bool CASM::Structure::read_species ( )

void CASM::Structure::reset ( )

virtual

clears symmetry, site internals, and other attributes

Should we also invalidate the occupants? for(Index i = 0; i < basis.size(); i++) { basis[i].site_occupant.set_value(-1); }

Reimplemented from CASM::BasicStructure< Site >.

Definition at line 385 of file Structure.cc.

void CASM::BasicStructure< Site >::set_basis ( Array< Site > basis_in )

inherited

Manually set the basis sites.

Allows for the basis elements of a basic structure to be manually set, e.g. as in jsonParser.cc.

void CASM::Structure::set_lattice	(	const Lattice &	lattice,
		COORD_TYPE	mode
	)

change the lattice and update site coordinates. Argument 'mode' specifies which mode is preserved e.g.: struc.set_lattice(new_lat, CART) calculates all Cartesian coordinates, invalidates the FRAC coordinates, and changes the lattice

Definition at line 664 of file Structure.cc.

void CASM::Structure::set_occs ( Array< int > occ_index )

Setting the current occupants of the structure to those specified by an array of integers.

Definition at line 1190 of file Structure.cc.

void CASM::BasicStructure< Site >::set_site_internals ( )

inherited

Associate each site with its basis index by setting its internal flags (asym_ind -> -1)

void CASM::Structure::sort_basis ( )

Rearrange basis by grouping atoms by type.

Loop through basis and rearrange atoms by type. Uses bubble sort algorithm by comparing integer values of the strings assigned to the basis occupants.

The basis gets sorted in a sort of alphabetical way, so be mindful of any POTCARs you might have if you run this.

Definition at line 858 of file Structure.cc.

Structure CASM::Structure::stack_on	(	const Structure &	understruc,
		bool	override = `0`
	)		const

Returns a heterostructre. The structure this function is called onto will be stretched to match a and b of the structure is it passed (understruc). The returned strucure will contain the basis of both structures, stacked on top of each other in the c direction.

This function only matches the ab planes.

Definition at line 692 of file Structure.cc.

Structure CASM::Structure::stamp_with	(	SiteCluster	stamp,
		bool	lat_override = `0`,
		bool	im_override = `0`
	)		const

Decorate your structure easily! Given a cluster, this routine will copy your structure and replace sites of the copy with sites from the cluster. Bedazzle! The lattice of your structure and cluster must be related by an integer matrix (supercell). Be mindful with the size of your stamped structure, it has to be big enough to fit the cluster.

Definition at line 888 of file Structure.cc.

void CASM::Structure::symmetrize ( const SymGroup & relaxed_factors )

Given a symmetry group, the basis of the structure will have each operation applied to it. The resulting set of basis from performing these operations will be averaged out, yielding a new average basis that will replace the current one.

Definition at line 1022 of file Structure.cc.

void CASM::Structure::symmetrize ( const double & tolerance )

Same as the other symmetrize routine, except this one assumes that the symmetry group you mean to use is the factor group of your structure within a certain tolerance.

Notice that the tolerance is also used on your point group!!

Definition at line 1069 of file Structure.cc.

jsonParser & CASM::Structure::to_json ( jsonParser & json ) const

Definition at line 1224 of file Structure.cc.

void CASM::BasicStructure< Site >::update ( )

inherited

void CASM::BasicStructure< Site >::within ( )

inherited

Translate all basis sites so that they are inside the unit cell.

Member Data Documentation

Array<Site > CASM::BasicStructure< Site >::basis

inherited

Lattice vectors that specifies periodicity of the crystal.

Definition at line 42 of file BasicStructure.hh.

SymGroupRepID CASM::Structure::basis_perm_rep_ID

mutableprotected

This holds the representation id of the permutation representation.

Definition at line 36 of file Structure.hh.

MasterSymGroup CASM::Structure::m_factor_group

mutableprotected

Group symmetry operations that map the lattice and basis of Structure onto themselves, assuming that the crystal is periodic

Definition at line 34 of file Structure.hh.

Lattice CASM::BasicStructure< Site >::m_lattice

protectedinherited

Definition at line 32 of file BasicStructure.hh.

bool CASM::Structure::SD_flag

protected

Specifies whether selectice dynamics is on or of for DFT calculations.

Definition at line 38 of file Structure.hh.

std::string CASM::BasicStructure< Site >::title

inherited

User-specified name of this Structure.

Definition at line 39 of file BasicStructure.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/Structure.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/crystallography/Structure.cc

Detailed Description

Public Member Functions

Public Attributes

Protected Attributes

Private Member Functions

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation