occ::crystal Namespace Reference

functionality related to periodic crystal structures, space groups, symmetry operations More...

Classes
struct	AsymmetricUnit
	A class representing an asymmetric unit of a crystal structure. More...
class	Crystal
	A class representing a crystal structure. More...
struct	CrystalAtomRegion
	A class representing a region of atoms in a crystal lattice. More...
struct	CrystalDimers
	A class representing the molecular dimers in a crystal lattice. More...
struct	CrystalSurfaceGenerationParameters
	Parameters for crystal surface generation. More...
struct	DimerIndex
	Represents a pair of sites in a crystal structure. More...
struct	DimerIndexHash
struct	DimerMappingEdge
class	DimerMappingTable
	Maps and manages symmetry relationships between dimers in a crystal. More...
struct	DimerMappingVertex
struct	HKL
	A struct representing a lattice vector triplet (h, k, l) in a crystal lattice. More...
class	ReciprocalAsymmetricUnit
struct	SiteIndex
struct	SiteIndexHash
struct	SiteMappingEdge
class	SiteMappingTable
struct	SiteMappingVertex
class	SpaceGroup
	This class represents a space group. More...
class	StandardBondLengths
	Standard hydrogen bond lengths for various elements. More...
class	Surface
	Represents and analyzes a crystal surface defined by Miller indices. More...
struct	SurfaceCutResult
	Results from analyzing a crystal surface cut. More...
struct	SymmetryDimerLabeller
class	SymmetryOperation
	Class representing a 3D symmetry operation. More...
struct	SymmetryOperationFormat
class	UnitCell
	This class represents a unit cell of a crystal lattice. More...

Typedefs
using	DimerMappingGraph = core::graph::Graph< DimerMappingVertex, DimerMappingEdge >
using	SiteMappingGraph = core::graph::Graph< SiteMappingVertex, SiteMappingEdge >
using	SGData = gemmi::SpaceGroup

Functions
Eigen::MatrixXd	muldin (const Eigen::VectorXd &x)
std::vector< Surface >	generate_surfaces (const Crystal &c, const CrystalSurfaceGenerationParameters &={})
UnitCell	cubic_cell (double length)
	Construct a cubic unit cell from a given length.
UnitCell	rhombohedral_cell (double length, double angle)
	Construct a rhombohedral unit cell from a given length and angle.
UnitCell	tetragonal_cell (double a, double c)
	Construct a tetragonal unit cell from two given lengths.
UnitCell	hexagonal_cell (double a, double c)
	Construct a hexagonal unit cell from two given lengths.
UnitCell	orthorhombic_cell (double a, double b, double c)
	Construct an orthorhombic unit cell from three given lengths.
UnitCell	monoclinic_cell (double a, double b, double c, double angle)
	Construct an orthorhombic unit cell from three given lengths and one angle.
UnitCell	triclinic_cell (double a, double b, double c, double alpha, double beta, double gamma)
	Construct an orthorhombic unit cell from three given lengths and three angles.
void	to_json (nlohmann::json &j, const CrystalDimers &)
void	from_json (const nlohmann::json &j, CrystalDimers &)
void	to_json (nlohmann::json &j, const AsymmetricUnit &)
void	from_json (const nlohmann::json &j, AsymmetricUnit &)
void	to_json (nlohmann::json &j, const UnitCell &)
void	from_json (const nlohmann::json &j, UnitCell &)
void	to_json (nlohmann::json &j, const CrystalAtomRegion &)
void	from_json (const nlohmann::json &j, CrystalAtomRegion &)

Detailed Description

functionality related to periodic crystal structures, space groups, symmetry operations

depends on occ::core and the gemmi library

Typedef Documentation

DimerMappingGraph

using occ::crystal::DimerMappingGraph = typedef core::graph::Graph<DimerMappingVertex, DimerMappingEdge>

SGData

using occ::crystal::SGData = typedef gemmi::SpaceGroup

SiteMappingGraph

using occ::crystal::SiteMappingGraph = typedef core::graph::Graph<SiteMappingVertex, SiteMappingEdge>

Function Documentation

cubic_cell()

UnitCell occ::crystal::cubic_cell

(

double

length

)

Construct a cubic unit cell from a given length.

from_json() [1/4]

void occ::crystal::from_json	(	const nlohmann::json &	j,
		AsymmetricUnit &
	)

from_json() [2/4]

void occ::crystal::from_json	(	const nlohmann::json &	j,
		CrystalAtomRegion &
	)

from_json() [3/4]

void occ::crystal::from_json	(	const nlohmann::json &	j,
		CrystalDimers &
	)

from_json() [4/4]

void occ::crystal::from_json	(	const nlohmann::json &	j,
		UnitCell &
	)

generate_surfaces()

std::vector< Surface > occ::crystal::generate_surfaces	(	const Crystal &	c,
		const CrystalSurfaceGenerationParameters &	= {}
	)

hexagonal_cell()

UnitCell occ::crystal::hexagonal_cell	(	double	a,
		double	c
	)

Construct a hexagonal unit cell from two given lengths.

monoclinic_cell()

UnitCell occ::crystal::monoclinic_cell	(	double	a,
		double	b,
		double	c,
		double	angle
	)

Construct an orthorhombic unit cell from three given lengths and one angle.

muldin()

Eigen::MatrixXd occ::crystal::muldin

(

const Eigen::VectorXd &

x

)

orthorhombic_cell()

UnitCell occ::crystal::orthorhombic_cell	(	double	a,
		double	b,
		double	c
	)

Construct an orthorhombic unit cell from three given lengths.

rhombohedral_cell()

UnitCell occ::crystal::rhombohedral_cell	(	double	length,
		double	angle
	)

Construct a rhombohedral unit cell from a given length and angle.

tetragonal_cell()

UnitCell occ::crystal::tetragonal_cell	(	double	a,
		double	c
	)

Construct a tetragonal unit cell from two given lengths.

to_json() [1/4]

void occ::crystal::to_json	(	nlohmann::json &	j,
		const AsymmetricUnit &
	)

to_json() [2/4]

void occ::crystal::to_json	(	nlohmann::json &	j,
		const CrystalAtomRegion &
	)

to_json() [3/4]

void occ::crystal::to_json	(	nlohmann::json &	j,
		const CrystalDimers &
	)

to_json() [4/4]

void occ::crystal::to_json	(	nlohmann::json &	j,
		const UnitCell &
	)

triclinic_cell()

UnitCell occ::crystal::triclinic_cell	(	double	a,
		double	b,
		double	c,
		double	alpha,
		double	beta,
		double	gamma
	)

Construct an orthorhombic unit cell from three given lengths and three angles.