cctbx/adptbx.h File Reference

#include <cctbx/uctbx.h>
#include <scitbx/matrix/eigensystem.h>
#include <scitbx/matrix/tensor_rank_2.h>
#include <scitbx/array_family/tiny_algebra.h>
#include <scitbx/type_holder.h>
#include <cctbx/error.h>

Go to the source code of this file.

Namespaces
namespace	cctbx
namespace	cctbx::adptbx
Classes
struct	factor_u_cart_u_iso
	Factorization into isotropic and remaining anisotropic contributions. More...
struct	factor_u_star_u_iso
	Factorization into isotropic and remaining anisotropic contributions. More...
struct	factor_u_cif_u_iso
	Factorization into isotropic and remaining anisotropic contributions. More...
struct	factor_beta_u_iso
	Factorization into isotropic and remaining anisotropic contributions. More...
class	eigensystem
	Group of associated eigenvectors and eigenvalues. More...
Functions
void	throw_not_positive_definite ()
double	u_as_b (double u_iso)
	Converts isotropic displacement parameter U -> B.
double	b_as_u (double b_iso)
	Converts isotropic displacement parameter B -> U.
template<typename FloatType>
sym_mat3< FloatType >	u_as_b (sym_mat3< FloatType > const &u_aniso)
	Converts anisotropic displacement parameters U -> B.
template<typename FloatType>
sym_mat3< FloatType >	b_as_u (sym_mat3< FloatType > const &b_aniso)
	Converts anisotropic displacement parameters B -> U.
template<typename FloatType>
sym_mat3< FloatType >	u_cif_as_u_star (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cif)
	Converts anisotropic displacement parameters u_cif -> u_star.
template<typename FloatType>
sym_mat3< FloatType >	u_star_as_u_cif (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_star)
	Converts anisotropic displacement parameters u_star -> u_cif.
template<typename FloatType>
sym_mat3< FloatType >	u_cart_as_u_star (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cart)
	Converts anisotropic displacement parameters u_cart -> u_star.
template<typename FloatType>
sym_mat3< FloatType >	u_star_as_u_cart (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_star)
	Converts anisotropic displacement parameters u_star -> u_cart.
template<typename FloatType>
sym_mat3< FloatType >	u_cart_as_u_cif (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cart)
	Converts anisotropic displacement parameters u_cart -> u_cif.
template<typename FloatType>
sym_mat3< FloatType >	u_cif_as_u_cart (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cif)
	Converts anisotropic displacement parameters u_cif -> u_cart.
template<typename FloatType>
sym_mat3< FloatType >	u_star_as_beta (sym_mat3< FloatType > const &u_star)
	Converts anisotropic displacement parameters u_star -> beta.
template<typename FloatType>
sym_mat3< FloatType >	beta_as_u_star (sym_mat3< FloatType > const &beta)
	Converts anisotropic displacement parameters beta -> u_star.
template<typename FloatType>
sym_mat3< FloatType >	u_cart_as_beta (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cart)
	Converts anisotropic displacement parameters u_cart -> beta.
template<typename FloatType>
sym_mat3< FloatType >	beta_as_u_cart (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &beta)
	Converts anisotropic displacement parameters beta -> u_cart.
template<typename FloatType>
sym_mat3< FloatType >	u_cif_as_beta (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cif)
	Converts anisotropic displacement parameters u_cif -> beta.
template<typename FloatType>
sym_mat3< FloatType >	beta_as_u_cif (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &beta)
	Converts anisotropic displacement parameters beta -> u_cif.
template<typename FloatType>
FloatType	u_cart_as_u_iso (sym_mat3< FloatType > const &u_cart)
	Converts anisotropic displacement parameters u_cart -> u_iso.
template<typename FloatType>
sym_mat3< FloatType >	u_iso_as_u_cart (FloatType const &u_iso)
	Converts u_iso -> anisotropic displacement parameters u_cart.
template<typename FloatType>
FloatType	u_star_as_u_iso (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_star)
	Converts u_star -> u_iso.
template<typename FloatType>
sym_mat3< FloatType >	u_iso_as_u_star (uctbx::unit_cell const &unit_cell, FloatType const &u_iso)
	Converts u_iso -> u_star.
template<typename FloatType>
FloatType	u_cif_as_u_iso (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &u_cif)
	Converts u_cif -> u_iso.
template<typename FloatType>
sym_mat3< FloatType >	u_iso_as_u_cif (uctbx::unit_cell const &unit_cell, FloatType const &u_iso)
	Converts u_iso -> u_cif.
template<typename FloatType>
FloatType	beta_as_u_iso (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &beta)
	Converts beta -> u_iso.
template<typename FloatType>
sym_mat3< FloatType >	u_iso_as_beta (uctbx::unit_cell const &unit_cell, FloatType const &u_iso)
	Converts u_iso -> beta.
double	debye_waller_factor_exp (const char *u_type, double arg, double max_arg=50)
	std::exp with upper limit for argument value.
double	debye_waller_factor_b_iso (double stol_sq, double b_iso)
	Isotropic Debye-Waller factor given (sin(theta)/lambda)^2 and b_iso.
double	debye_waller_factor_u_iso (double stol_sq, double u_iso)
	Isotropic Debye-Waller factor given (sin(theta)/lambda)^2 and u_iso.
double	debye_waller_factor_b_iso (uctbx::unit_cell const &unit_cell, miller::index<> const &h, double b_iso)
	Isotropic Debye-Waller factor given a Miller index and b_iso.
double	debye_waller_factor_u_iso (uctbx::unit_cell const &unit_cell, miller::index<> const &h, double u_iso)
	Isotropic Debye-Waller factor given a Miller index and u_iso.
template<typename FloatType>
FloatType	debye_waller_factor_u_star (miller::index<> const &h, sym_mat3< FloatType > const &u_star)
	Anisotropic Debye-Waller factor given a Miller index and u_star.
template<typename NumType>
sym_mat3< NumType >	debye_waller_factor_u_star_gradient_coefficients (miller::index<> const &h, scitbx::type_holder< NumType > holder=scitbx::type_holder< NumType >())
	Coefficients for gradients of Debye-Waller factor w.r.t. u_star.
template<typename NumType>
af::shared< NumType >	debye_waller_factor_u_star_curvature_coefficients (miller::index<> const &h, scitbx::type_holder< NumType >)
	Coefficients for curvatures of Debye-Waller factor w.r.t. u_star.
template<typename FloatType>
FloatType	debye_waller_factor_beta (miller::index<> const &h, sym_mat3< FloatType > const &beta)
	Anisotropic Debye-Waller factor given a Miller index and beta.
template<typename FloatType>
FloatType	debye_waller_factor_u_cif (uctbx::unit_cell const &unit_cell, miller::index<> const &h, sym_mat3< FloatType > const &u_cif)
	Anisotropic Debye-Waller factor given a Miller index and u_cif.
template<typename FloatType>
FloatType	debye_waller_factor_u_cart (uctbx::unit_cell const &unit_cell, miller::index<> const &h, sym_mat3< FloatType > const &u_cart)
	Anisotropic Debye-Waller factor given a Miller index and u_cart.
template<typename FloatType>
sym_mat3< FloatType >	grad_u_star_as_u_cart (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &grad_u_star)
	Transformation of gradients w.r.t. u_star to gradients w.r.t. u_cart.
template<typename FloatType>
af::shared< sym_mat3< FloatType > >	grad_u_star_as_u_cart (uctbx::unit_cell const &unit_cell, af::const_ref< sym_mat3< FloatType > > const &grad_u_star)
	Transformation of gradients w.r.t. u_star to gradients w.r.t. u_cart.
template<typename FloatType>
sym_mat3< FloatType >	grad_u_cart_as_u_star (uctbx::unit_cell const &unit_cell, sym_mat3< FloatType > const &grad_u_cart)
	Transformation of gradients w.r.t. u_cart to gradients w.r.t. u_star.
template<typename FloatType>
af::shared< sym_mat3< FloatType > >	grad_u_cart_as_u_star (uctbx::unit_cell const &unit_cell, af::const_ref< sym_mat3< FloatType > > const &grad_u_cart)
	Transformation of gradients w.r.t. u_cart to gradients w.r.t. u_star.
template<typename FloatType>
vec3< FloatType >	eigenvalues (sym_mat3< FloatType > const &adp)
	Determines the eigenvalues of the anisotropic displacement tensor.
template<typename FloatType>
bool	is_positive_definite (vec3< FloatType > const &adp_eigenvalues)
	Tests if the anisotropic displacement tensor is positive definite, given adp_eigenvalues.
template<typename FloatType>
bool	is_positive_definite (vec3< FloatType > const &adp_eigenvalues, FloatType const &tolerance)
	Tests if the anisotropic displacement tensor is positive definite, given adp_eigenvalues.
template<typename FloatType>
bool	is_positive_definite (sym_mat3< FloatType > const &adp)
	Tests if the anisotropic displacement tensor is positive definite.
template<typename FloatType>
bool	is_positive_definite (sym_mat3< FloatType > const &adp, FloatType const &tolerance)
	Tests if the anisotropic displacement tensor is positive definite.
template<typename FloatType>
af::shared< bool >	is_positive_definite (af::const_ref< sym_mat3< FloatType > > const &adp, FloatType const &tolerance)
	True if adp is positive definite, else False.
template<typename FloatType>
sym_mat3< FloatType >	eigenvalue_filtering (sym_mat3< FloatType > const &u_cart, FloatType const &u_min=0, FloatType const &u_max=0)
	Modifies u_cart such that all eigenvalues are >= u_min and <= u_max.
template<typename FloatType>
sym_mat3< FloatType >	c_u_c_transpose (mat3< FloatType > const &c, sym_mat3< FloatType > const &u)
	Tensor transformation: c * u * c.transpose().

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Detailed Description

Toolbox for the handling of anisotropic displacement parameters (ADPs).