IntegralCluster

Detailed Description

Functions and classes related to IntegralCluster.

Modules
	ClusterOrbits
	Functions and classes for IntegralCluster orbits of any type.
	ClusterSpecs
	ClusterSpecs Generate IntegralCluster orbits of specific types.
	ClusterSymCompare
	Functions and classes for creating cluster SymCompare functors for orbit generation .
	IntegralClusterOrbits
	Traits and functions for specific types of IntegralCluster orbits.

Classes
class	CASM::OrbitBranchSpecs< _OrbitType >
	Store data used to generate an orbit branch of IntegralCluster. More...

Functions
template<typename OutputIterator >
OutputIterator	CASM::prim_periodic_orbit_neighborhood (const PrimPeriodicOrbit< IntegralCluster > &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	CASM::prim_periodic_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OutputIterator , typename OrbitType >
OutputIterator	CASM::flower_neighborhood (OrbitType const &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	CASM::flower_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OutputIterator >
OutputIterator	CASM::neighborhood (Structure const &unit, double max_radius, SiteFilterFunction site_filter, OutputIterator result, double xtal_tol)
	Output the neighborhood of UnitCellCoord within max_radius of any sites in unit cell. More...
template<typename OutputIterator >
OutputIterator	CASM::neighborhood (IntegralCluster const &phenomenal, double cutoff_radius, SiteFilterFunction site_filter, bool include_phenomenal_sites, OutputIterator result, double xtal_tol)
	Output the neighborhood of sites within cutoff_radius of any sites in the phenomenal. More...
template<typename OrbitType , typename OutputIterator >
OutputIterator	CASM::local_orbit_neighborhood (const OrbitType &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	CASM::local_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OrbitType >
OrbitGenerators< OrbitType > &	CASM::insert_subcluster_generators (typename OrbitType::Element cluster, OrbitGenerators< OrbitType > &generators)
	Given a cluster, generate all subcluster generators. More...
template<typename OrbitType , typename OrbitInputIterator , typename OrbitOutputIterator >
OrbitOutputIterator	CASM::make_next_orbitbranch (OrbitInputIterator begin, OrbitInputIterator end, const OrbitBranchSpecs< OrbitType > &specs, OrbitOutputIterator result, std::ostream &status)
	Use orbits of size n to generate orbits of size n+1. More...

Function Documentation

flower_neighborhood() [1/2]

template<typename ClusterOrbitIterator , typename OutputIterator >

OutputIterator CASM::flower_neighborhood	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		OutputIterator	result
	)

Iterate over all sites in all orbits and insert a UnitCellCoord.

Parameters

begin,end	Range of PrimPeriodicOrbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters. Respects translational properties of local orbits, so can be used when translational type is unknown.

Parameters

begin,end	Range of PrimPeriodicOrbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters.

Definition at line 816 of file ClusterOrbits_impl.hh.

flower_neighborhood() [2/2]

template<typename OutputIterator , typename OrbitType >

OutputIterator CASM::flower_neighborhood	(	OrbitType const &	orbit,
		OutputIterator	result
	)

Iterate over all sites in an orbit and insert a UnitCellCoord.

Parameters

orbit	an PrimPeriodicOrbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters. Respects translational properties of local orbits, so can be used when translational type is unknown.

Parameters

orbit	an PrimPeriodicOrbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters.

Definition at line 764 of file ClusterOrbits_impl.hh.

insert_subcluster_generators()

template<typename OrbitType >

OrbitGenerators< OrbitType > & CASM::insert_subcluster_generators	(	typename OrbitType::Element	cluster,
		OrbitGenerators< OrbitType > &	generators
	)

Given a cluster, generate all subcluster generators.

Parameters

cluster	A cluster to generate subclusters of
generators	An OrbitGeneratorSet<OrbitType>& to store generating elements for subclusters of cluster
stutus	Stream for status messages

Uses SymCompareType::compare to find unique generating elements

Definition at line 250 of file ClusterOrbits_impl.hh.

local_neighborhood()

template<typename ClusterOrbitIterator , typename OutputIterator >

OutputIterator CASM::local_neighborhood	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		OutputIterator	result
	)

Iterate over all sites in all orbits and insert a UnitCellCoord.

Parameters

begin,end	Range of Orbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

This simply outputs all UnitCellCoord in all equivalent clusters of each orbit

Definition at line 178 of file ClusterOrbits_impl.hh.

local_orbit_neighborhood()

template<typename OrbitType , typename OutputIterator >

OutputIterator CASM::local_orbit_neighborhood	(	const OrbitType &	orbit,
		OutputIterator	result
	)

Iterate over all sites in an orbit and insert a UnitCellCoord.

Parameters

orbit	an Orbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord in all equivalent clusters

Definition at line 157 of file ClusterOrbits_impl.hh.

make_next_orbitbranch()

template<typename OrbitType , typename OrbitInputIterator , typename OrbitOutputIterator >

OrbitOutputIterator CASM::make_next_orbitbranch	(	OrbitInputIterator	begin,
		OrbitInputIterator	end,
		const OrbitBranchSpecs< OrbitType > &	specs,
		OrbitOutputIterator	result,
		std::ostream &	status
	)

Use orbits of size n to generate orbits of size n+1.

Parameters

begin,end	A range of input orbits of size n
specs	OrbitBranchSpecs for orbits of size n+1
result	An output iterator for orbits of IntegralCluster
stutus	Stream for status messages

Construct an OrbitGenerators object to collect orbit generating elements

Use OrbitBranchSpecs to insert orbit generating elements for the next orbitbranch

Generate orbits from the orbit generating elements

Construct an OrbitGenerators object to collect orbit generating elements

Use OrbitBranchSpecs to insert orbit generating elements for the next orbitbranch

Generate orbits from the orbit generating elements

Definition at line 453 of file ClusterOrbits_impl.hh.

neighborhood() [1/2]

template<typename OutputIterator >

OutputIterator CASM::neighborhood	(	IntegralCluster const &	phenomenal,
		double	cutoff_radius,
		SiteFilterFunction	site_filter,
		bool	include_phenomenal_sites,
		OutputIterator	result,
		double	xtal_tol
	)

Output the neighborhood of sites within cutoff_radius of any sites in the phenomenal.

Parameters

phenomenal	IntegralCluster
cutoff_radius	The neighborhood distance cutoff
site_filter	A filter function that returns true for UnitCellCoord that should be considered for the neighborhood
result	Output iterator for container of UnitCellCoord
xtal_tol	Crystallography tolerance used to contstruct UnitCellCoord

Returns

Output iterator after generating the neighborhood

lattice scaling

lattice scaling

Definition at line 83 of file ClusterOrbits_impl.hh.

neighborhood() [2/2]

template<typename OutputIterator >

OutputIterator CASM::neighborhood	(	Structure const &	unit,
		double	max_radius,
		SiteFilterFunction	site_filter,
		OutputIterator	result,
		double	xtal_tol
	)

Output the neighborhood of UnitCellCoord within max_radius of any sites in unit cell.

Output the neighborhood of UnitCellCoord within max_radius of any site in unit cell.

Parameters

unit	The unit cell Structure
max_radius	The neighborhood distance cutoff
site_filter	A filter function that returns true for CoordType that should be considered for the neighborhood
result	Output iterator for container of UnitCellCoord
xtal_tol	Crystallography tolerance used to contstruct UnitCellCoord from CoordType

Returns

Output iterator after generating the neighborhood

Definition at line 38 of file ClusterOrbits_impl.hh.

prim_periodic_neighborhood()

template<typename ClusterOrbitIterator , typename OutputIterator >

OutputIterator CASM::prim_periodic_neighborhood	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		OutputIterator	result
	)

Iterate over all sites in all orbits and insert a UnitCellCoord.

Parameters

begin,end	Range of PrimPeriodicOrbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters.

Parameters

begin,end	Range of Orbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters.

Definition at line 740 of file ClusterOrbits_impl.hh.

prim_periodic_orbit_neighborhood()

template<typename OutputIterator >

OutputIterator CASM::prim_periodic_orbit_neighborhood	(	const PrimPeriodicOrbit< IntegralCluster > &	orbit,
		OutputIterator	result
	)

Iterate over all sites in an orbit and insert a UnitCellCoord.

Parameters

orbit	an Orbit<IntegralCluster>
result	an OutputIterator for UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It uses all clusters that touch origin unitcell, including translationally equivalent clusters.

Definition at line 709 of file ClusterOrbits_impl.hh.