cctbx::xray Namespace Reference

X-ray scatterer and structure factor namespace. More...

Classes
struct	f_sq_as_f_xtal_3_7
struct	f_sq_as_f_crystals
struct	f_as_f_sq
struct	array_f_sq_as_f
struct	array_f_as_f_sq
class	fast_gradients
struct	gradient_flags
class	sampled_model_density
class	sampling_base
class	scatterer
	Information about an atom that is needed for a structure factor calculation. More...
struct	scatterer_flags
class	grad_flags_counts_core
class	scatterer_grad_flags_counts
class	grad_flags_counts
class	apply_rigid_body_shift
class	scattering_type_registry
Namespaces
namespace	targets
	X-ray target function of structure factors namespace.
Functions
double	calc_u_base (double d_min, double grid_resolution_factor, double quality_factor=100, double max_u_base=adptbx::b_as_u(1000))
	Artificial temperature factor for the treatment of aliasing problems.
template<typename FloatType>
void	apply_u_extra (uctbx::unit_cell const &unit_cell, FloatType const &u_extra, miller::index<> const &miller_index, std::complex< FloatType > &structure_factor, FloatType const &multiplier)
template<typename FloatType>
void	apply_u_extra (uctbx::unit_cell const &unit_cell, FloatType const &u_extra, af::const_ref< miller::index<> > const &miller_indices, af::ref< std::complex< FloatType > > const &structure_factors, FloatType const &multiplier=1)
template<typename ScattererType>
void	set_scatterer_grad_flags (af::ref< ScattererType > const &scatterers, bool site=false, bool u_iso=false, bool u_aniso=false, bool occupancy=false, bool fp=false, bool fdp=false, bool tan_u_iso=false, int param=0)
	Set the flags of each given scatterers to the given values.
template<typename ScattererType>
void	flags_set_grads (af::ref< ScattererType > const &self, bool state)
template<typename ScattererType>
af::shared< bool >	is_positive_definite_u (af::const_ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell)
template<typename ScattererType>
af::shared< bool >	is_positive_definite_u (af::const_ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell, double u_cart_tolerance)
template<typename ScattererType>
void	tidy_us (af::ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell, sgtbx::site_symmetry_table const &site_symmetry_table, double u_min, double u_max)
template<typename ScattererType>
void	u_star_plus_u_iso (af::ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell)
template<typename ScattererType>
void	shift_us (af::ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell, double u_shift)
template<typename ScattererType>
void	shift_us (af::ref< ScattererType > const &scatterers, uctbx::unit_cell const &unit_cell, double u_shift, af::const_ref< std::size_t > const &selection)
template<typename ScattererType>
void	shift_occupancies (af::ref< ScattererType > const &scatterers, double q_shift, af::const_ref< std::size_t > const &selection)
template<typename ScattererType>
void	shift_occupancies (af::ref< ScattererType > const &scatterers, double q_shift)
template<typename ScattererType>
void	apply_symmetry_sites (sgtbx::site_symmetry_table const &site_symmetry_table, af::ref< ScattererType > const &scatterers)
template<typename ScattererType>
void	apply_symmetry_u_stars (sgtbx::site_symmetry_table const &site_symmetry_table, af::ref< ScattererType > const &scatterers, double u_star_tolerance=0)
template<typename ScattererType>
void	add_scatterers_ext (uctbx::unit_cell const &unit_cell, sgtbx::space_group const &space_group, af::ref< ScattererType > const &scatterers, sgtbx::site_symmetry_table &site_symmetry_table, sgtbx::site_symmetry_table const &site_symmetry_table_for_new, double min_distance_sym_equiv, double u_star_tolerance, bool assert_min_distance_sym_equiv)
template<typename ScattererType>
af::shared< ScattererType >	change_basis (af::const_ref< ScattererType > const &scatterers, sgtbx::change_of_basis_op const &cb_op)
template<typename ScattererType>
af::shared< ScattererType >	expand_to_p1 (uctbx::unit_cell const &unit_cell, sgtbx::space_group const &space_group, af::const_ref< ScattererType > const &scatterers, sgtbx::site_symmetry_table const &site_symmetry_table, bool append_number_to_labels)
template<typename ScattererType>
std::size_t	n_undefined_multiplicities (af::const_ref< ScattererType > const &scatterers)
template<typename AsuMappingsType, typename ScattererType>
void	asu_mappings_process (AsuMappingsType &asu_mappings, af::const_ref< ScattererType > const &scatterers, sgtbx::site_symmetry_table const &site_symmetry_table)
template<typename ScattererType>
af::shared< ScattererType >	rotate (uctbx::unit_cell const &unit_cell, scitbx::mat3< double > const &rotation_matrix, af::const_ref< ScattererType > const &scatterers)
template<class ScattererType, class TableType>
void	set_inelastic_form_factors (af::ref< ScattererType > const &scatterers, eltbx::wavelengths::characteristic photon, bool set_use_fp_fdp)

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Detailed Description

X-ray scatterer and structure factor namespace.

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Function Documentation

double cctbx::xray::calc_u_base	(	double	d_min,
		double	grid_resolution_factor,
		double	quality_factor = 100,
		double	max_u_base = adptbx::b_as_u(1000)
	)			[inline]

Artificial temperature factor for the treatment of aliasing problems.

Reference:

Gerard Bricogne (2001), International Tables for Crystallography, Volume B, 2001, p. 87 (end of section 1.3.4.4.5).

Parameters:

	d_min	= 1/d*max
	grid_resolution_factor	= 1/(2*sigma)
	quality_factor	= Q
	max_u_base	is a user-defined upper limit.

quality_factor = 100 for 1% accuracy.

See also: cctbx::uctbx::unit_cell::d()

References cctbx::adptbx::b_as_u(), and CCTBX_ASSERT.

void cctbx::xray::set_scatterer_grad_flags	(	af::ref< ScattererType > const &	scatterers,
		bool	site = false,
		bool	u_iso = false,
		bool	u_aniso = false,
		bool	occupancy = false,
		bool	fp = false,
		bool	fdp = false,
		bool	tan_u_iso = false,
		int	param = 0
	)			[inline]

Set the flags of each given scatterers to the given values.

The logic is as follow:

1. if a scatterer is not used (the 'use' flag is false), no flag is set;
2. the grad_u_iso flag (as well as the tan_u_iso flag)
   1. is set to the specified value only if the use_u_iso flag is set;
   2. otherwise it is set to false;
3. the same logic applies for grad_u_aniso and use_u_aniso;
4. the use_fp_fdp flag
   1. is set iff either grad_fp or grad_fdp is set;
   2. otherwise it is left unchanged.

References CCTBX_ASSERT.