cell.h File Reference

Data Structures
struct	rvec
struct	g6

Typedefs
typedef struct _unitcell	UnitCell

Enumerations
enum	LatticeType {   L_TRICLINIC ,   L_MONOCLINIC ,   L_ORTHORHOMBIC ,   L_TETRAGONAL ,   L_RHOMBOHEDRAL ,   L_HEXAGONAL ,   L_CUBIC }

Functions
UnitCell *	cell_new (void)
UnitCell *	cell_new_from_cell (const UnitCell *orig)
void	cell_free (UnitCell *cell)
UnitCell *	cell_new_from_parameters (double a, double b, double c, double alpha, double beta, double gamma)
UnitCell *	cell_new_from_reciprocal_axes (struct rvec as, struct rvec bs, struct rvec cs)
UnitCell *	cell_new_from_direct_axes (struct rvec as, struct rvec bs, struct rvec cs)
int	cell_has_parameters (const UnitCell *cell)
void	cell_set_cartesian (UnitCell *cell, double ax, double ay, double az, double bx, double by, double bz, double cx, double cy, double cz)
void	cell_set_parameters (UnitCell *cell, double a, double b, double c, double alpha, double beta, double gamma)
int	cell_get_parameters (UnitCell *cell, double *a, double *b, double *c, double *alpha, double *beta, double *gamma)
int	cell_get_cartesian (UnitCell *cell, double *ax, double *ay, double *az, double *bx, double *by, double *bz, double *cx, double *cy, double *cz)
int	cell_get_reciprocal (UnitCell *cell, double *asx, double *asy, double *asz, double *bsx, double *bsy, double *bsz, double *csx, double *csy, double *csz)
void	cell_set_reciprocal (UnitCell *cell, double asx, double asy, double asz, double bsx, double bsy, double bsz, double csx, double csy, double csz)
LatticeType	cell_get_lattice_type (const UnitCell *cell)
void	cell_set_lattice_type (UnitCell *cell, LatticeType lattice_type)
struct g6	cell_get_G6 (UnitCell *cell)
char	cell_get_centering (const UnitCell *cell)
void	cell_set_centering (UnitCell *cell, char centering)
char	cell_get_unique_axis (const UnitCell *cell)
void	cell_set_unique_axis (UnitCell *cell, char unique_axis)
UnitCell *	cell_transform_gsl_direct (UnitCell *in, gsl_matrix *m)
UnitCell *	cell_rotate_gsl_direct (UnitCell *in, gsl_matrix *m)
UnitCell *	cell_transform_rational (UnitCell *cell, RationalMatrix *m)
UnitCell *	cell_transform_rational_inverse (UnitCell *cell, RationalMatrix *m)
UnitCell *	cell_transform_intmat (UnitCell *cell, IntegerMatrix *m)
UnitCell *	cell_transform_intmat_inverse (UnitCell *cell, IntegerMatrix *m)

Detailed Description

Unit cell structure

Typedef Documentation

UnitCell

typedef struct _unitcell UnitCell

Opaque data structure representing a unit cell.

This data structure is opaque. You must use the available accessor functions to read and write its contents.

Enumeration Type Documentation

LatticeType

enum LatticeType

An enumeration of the possible lattice types: triclinic, monoclinic, orthorhombic, tetragonal, rhombohedral, hexagonal and cubic.

Function Documentation

cell_free()

void cell_free ( UnitCell * cell )

extern

Parameters

cell	A UnitCell to free.

Frees a UnitCell, and all internal resources concerning that cell.

cell_has_parameters()

int cell_has_parameters ( const UnitCell * cell )

extern

Parameters

cell	A UnitCell

Returns

True if cell has its parameters specified.

cell_new()

UnitCell * cell_new ( void )

extern

Create a new UnitCell.

Returns

the new unit cell, or NULL on failure.

cell_rotate_gsl_direct()

UnitCell * cell_rotate_gsl_direct ( UnitCell * in, gsl_matrix * m )

extern

Parameters

in	A UnitCell
m	A GSL matrix

Transforms in by altering the cartesian axes according to m. Note that this is not the same as cell_transform_gsl_direct(), because that routine transforms the crystallographic axes whereas this one transforms the cartesian axes - the order of matrix multiplication is opposite.

This routine has its name because the usual application of this type of transformation is to rotate a unit cell in 3D space. Other types of transformation, e.g. including a stretch or shear of space, are possible but don't make much crystallographic sense.

Returns

a newly-allocated transformed UnitCell.

cell_transform_gsl_direct()

UnitCell * cell_transform_gsl_direct ( UnitCell * in, gsl_matrix * m )

extern

Parameters

in	A UnitCell
m	A GSL matrix

Transforms in by combining the crystallographic axes as described by m. See doc/matrix-notation.pdf, equation 1.

Returns

a newly-allocated transformed UnitCell.

cell_transform_intmat()

UnitCell * cell_transform_intmat ( UnitCell * cell, IntegerMatrix * m )

extern

Parameters

cell	A UnitCell.
m	An IntegerMatrix.

Applies m to cell.

This is just a convenience function which turns m into a RationalMatrix and then calls cell_transform_rational(). See the documentation for that function for some important information.

Returns

Transformed copy of cell.

cell_transform_intmat_inverse()

UnitCell * cell_transform_intmat_inverse ( UnitCell * cell, IntegerMatrix * m )

extern

Parameters

cell	A UnitCell.
m	An IntegerMatrix

Applies the inverse of m to cell.

Returns

Transformed copy of cell.

cell_transform_rational()

UnitCell * cell_transform_rational ( UnitCell * cell, RationalMatrix * m )

extern

Parameters

cell	A UnitCell.
m	A RationalMatrix.

Applies m to cell.

This function will determine the centering of the resulting unit cell, producing '?' if any lattice points cannot be accounted for. Note that if there are 'excess' lattice points in the transformed cell, the centering will still be '?' even if the lattice points for another centering are all present.

The lattice type will be set to triclinic, and the unique axis to '?'.

Returns

Transformed copy of cell.

cell_transform_rational_inverse()

UnitCell * cell_transform_rational_inverse ( UnitCell * cell, RationalMatrix * m )

extern

Parameters

cell	A UnitCell.
m	A RationalMatrix

Applies the inverse of m to cell.

Returns

Transformed copy of cell.