cctbx::adptbx Namespace Reference

ADP (anisotropic displacement parameters) Toolbox namespace. More...


Classes

class  mean_square_displacement
 Mean square displacement along a direction. More...
class  relative_hirshfeld_difference
 Relative difference of the mean square displacements of two scatterers. More...
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...
class  projection_sum

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 arg_limit, bool truncate_exp_arg)
 std::exp with upper limit for argument value.
double debye_waller_factor_b_iso (double stol_sq, double b_iso, double exp_arg_limit=50, bool truncate_exp_arg=false)
 Isotropic Debye-Waller factor given (sin(theta)/lambda)^2 and b_iso.
template<typename FloatType>
af::shared< FloatType > debye_waller_factor_b_iso (af::const_ref< double > const &stol_sq, FloatType const &b_iso, FloatType const &exp_arg_limit=50, bool truncate_exp_arg=false)
 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, FloatType const &exp_arg_limit=50, bool truncate_exp_arg=false)
 Anisotropic Debye-Waller factor given a Miller index and u_star.
template<typename FloatType>
af::shared< FloatType > debye_waller_factor_u_star (af::const_ref< miller::index<> > const &miller_indices, sym_mat3< FloatType > const &u_star, FloatType const &exp_arg_limit=50, bool truncate_exp_arg=false)
 Anisotropic Debye-Waller factor given a Miller indices 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 > isotropize (sym_mat3< FloatType > const &u_cart, FloatType const &anisotropy_min=0.25)
 Isotropize u_cart: modify u_cart such that it meets target anisotropy.
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().


Detailed Description

ADP (anisotropic displacement parameters) Toolbox namespace.

Function Documentation

sym_mat3<FloatType> cctbx::adptbx::beta_as_u_cart ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  beta 
) [inline]

Converts anisotropic displacement parameters beta -> u_cart.

Implemented as u_star_as_u_cart(unit_cell, beta_as_u_star(beta)).

References beta_as_u_star(), and u_star_as_u_cart().

Referenced by beta_as_u_iso().

sym_mat3<FloatType> cctbx::adptbx::beta_as_u_cif ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  beta 
) [inline]

Converts anisotropic displacement parameters beta -> u_cif.

Implemented as u_star_as_u_cif(unit_cell, beta_as_u_star(beta)).

References beta_as_u_star(), and u_star_as_u_cif().

FloatType cctbx::adptbx::beta_as_u_iso ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  beta 
) [inline]

Converts beta -> u_iso.

Implemented as u_cart_as_u_iso(beta_as_u_cart(unit_cell, beta)).

References beta_as_u_cart(), and u_cart_as_u_iso().

sym_mat3<FloatType> cctbx::adptbx::beta_as_u_star ( sym_mat3< FloatType > const &  beta  )  [inline]

Converts anisotropic displacement parameters beta -> u_star.

The elements of beta are divided by 2pi^2.

Referenced by beta_as_u_cart(), beta_as_u_cif(), and debye_waller_factor_beta().

sym_mat3<FloatType> cctbx::adptbx::c_u_c_transpose ( mat3< FloatType > const &  c,
sym_mat3< FloatType > const &  u 
) [inline]

Tensor transformation: c * u * c.transpose().

For use in Python only.

References sym_mat3::tensor_transform().

af::shared<NumType> cctbx::adptbx::debye_waller_factor_u_star_curvature_coefficients ( miller::index<> const &  h,
scitbx::type_holder< NumType >   
) [inline]

Coefficients for curvatures of Debye-Waller factor w.r.t. u_star.

Formula for the curvatures: (-2*pi**2)**2 * debye_waller_factor_u_star(h, u_star) * result

The returned array contains the 6*(6+1)/2 elements of the upper diagonal of the (6 x 6) matrix of curvatures.

sym_mat3<NumType> cctbx::adptbx::debye_waller_factor_u_star_gradient_coefficients ( miller::index<> const &  h,
scitbx::type_holder< NumType >  holder = scitbx::type_holder<NumType>() 
) [inline]

Coefficients for gradients of Debye-Waller factor w.r.t. u_star.

Formula for the gradients: -2*pi**2 * debye_waller_factor_u_star(h, u_star) * result

It should be noted that passing a 2nd argument, e.g.

        debye_waller_factor_u_star_gradient_coefficients(
          h, scitbx::type_holder<double>());
to select the version returning sym_mat3<double>, is deprecated. All the platform supported by the cctbx have C++ compiler which accepts the simpler syntax
        debye_waller_factor_u_star_gradient_coefficients<double>(h)
The last one which failed to support such function template specialisation, VC++ 7.1, has been dropped in early 2009.

Referenced by in_origin_centric_space_group::compute_anisotropic_part(), and in_generic_space_group::compute_anisotropic_part().

sym_mat3<FloatType> cctbx::adptbx::eigenvalue_filtering ( sym_mat3< FloatType > const &  u_cart,
FloatType const &  u_min = 0,
FloatType const &  u_max = 0 
) [inline]

Modifies u_cart such that all eigenvalues are >= u_min and <= u_max.

u_max is used only if it is greater than zero.

Referenced by scatterer< float_type >::tidy_u().

vec3<FloatType> cctbx::adptbx::eigenvalues ( sym_mat3< FloatType > const &  adp  )  [inline]

Determines the eigenvalues of the anisotropic displacement tensor.

Equivalent to eigensystem<>().values().

Referenced by is_positive_definite().

af::shared<sym_mat3<FloatType> > cctbx::adptbx::grad_u_cart_as_u_star ( uctbx::unit_cell const &  unit_cell,
af::const_ref< sym_mat3< FloatType > > const &  grad_u_cart 
) [inline]

Transformation of gradients w.r.t. u_cart to gradients w.r.t. u_star.

Vector version.

References grad_u_cart_as_u_star().

sym_mat3<FloatType> cctbx::adptbx::grad_u_cart_as_u_star ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  grad_u_cart 
) [inline]

Transformation of gradients w.r.t. u_cart to gradients w.r.t. u_star.

Scalar version.

References scitbx::matrix::tensor_rank_2::gradient_transform(), and unit_cell::orthogonalization_matrix().

Referenced by grad_u_cart_as_u_star().

af::shared<sym_mat3<FloatType> > cctbx::adptbx::grad_u_star_as_u_cart ( uctbx::unit_cell const &  unit_cell,
af::const_ref< sym_mat3< FloatType > > const &  grad_u_star 
) [inline]

Transformation of gradients w.r.t. u_star to gradients w.r.t. u_cart.

Vector version.

References grad_u_star_as_u_cart().

sym_mat3<FloatType> cctbx::adptbx::grad_u_star_as_u_cart ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  grad_u_star 
) [inline]

Transformation of gradients w.r.t. u_star to gradients w.r.t. u_cart.

Scalar version.

References unit_cell::fractionalization_matrix(), and scitbx::matrix::tensor_rank_2::gradient_transform().

Referenced by grad_u_star_as_u_cart().

af::shared<bool> cctbx::adptbx::is_positive_definite ( af::const_ref< sym_mat3< FloatType > > const &  adp,
FloatType const &  tolerance 
) [inline]

True if adp is positive definite, else False.

Tests if all eigenvalues(adp) are >= -tolerance.

References eigenvalues(), and is_positive_definite().

Referenced by scatterer< float_type >::is_positive_definite_u().

bool cctbx::adptbx::is_positive_definite ( sym_mat3< FloatType > const &  adp,
FloatType const &  tolerance 
) [inline]

Tests if the anisotropic displacement tensor is positive definite.

Tests if all eigenvalues(adp) are >= -tolerance.

References eigenvalues(), and is_positive_definite().

bool cctbx::adptbx::is_positive_definite ( sym_mat3< FloatType > const &  adp  )  [inline]

Tests if the anisotropic displacement tensor is positive definite.

Tests if all eigenvalues(adp) are > 0.

References eigenvalues(), and is_positive_definite().

bool cctbx::adptbx::is_positive_definite ( vec3< FloatType > const &  adp_eigenvalues,
FloatType const &  tolerance 
) [inline]

Tests if the anisotropic displacement tensor is positive definite, given adp_eigenvalues.

Tests if all adp_eigenvalues are >= -tolerance.

See also: eigenvalues().

bool cctbx::adptbx::is_positive_definite ( vec3< FloatType > const &  adp_eigenvalues  )  [inline]

Tests if the anisotropic displacement tensor is positive definite, given adp_eigenvalues.

Tests if all adp_eigenvalues are > 0.

See also: eigenvalues().

Referenced by is_positive_definite().

sym_mat3<FloatType> cctbx::adptbx::u_cart_as_beta ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cart 
) [inline]

Converts anisotropic displacement parameters u_cart -> beta.

Implemented as u_star_as_beta(u_cart_as_u_star(unit_cell, u_cart)).

References u_cart_as_u_star(), and u_star_as_beta().

Referenced by u_iso_as_beta().

sym_mat3<FloatType> cctbx::adptbx::u_cart_as_u_cif ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cart 
) [inline]

Converts anisotropic displacement parameters u_cart -> u_cif.

Implemented without a significant loss of efficiency as u_star_as_u_cif(unit_cell, u_cart_as_u_star(unit_cell, u_cart)).

References u_cart_as_u_star(), and u_star_as_u_cif().

Referenced by u_iso_as_u_cif().

FloatType cctbx::adptbx::u_cart_as_u_iso ( sym_mat3< FloatType > const &  u_cart  )  [inline]

Converts anisotropic displacement parameters u_cart -> u_iso.

u_iso is defined as the mean of the diagonal elements of u_cart:

          u_iso = 1/3 (u_cart_11 + u_cart_22 + u_cart_33)

Referenced by beta_as_u_iso(), u_cif_as_u_iso(), and u_star_as_u_iso().

sym_mat3<FloatType> cctbx::adptbx::u_cart_as_u_star ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cart 
) [inline]

Converts anisotropic displacement parameters u_cart -> u_star.

The formula for the transformation is u_star = c * u_cart * c.transpose(), with c = unit_cell.fractionalization_matrix().

References unit_cell::fractionalization_matrix(), and sym_mat3::tensor_transform().

Referenced by debye_waller_factor_u_cart(), scatterer< float_type >::tidy_u(), u_cart_as_beta(), u_cart_as_u_cif(), and u_iso_as_u_star().

sym_mat3<FloatType> cctbx::adptbx::u_cif_as_beta ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cif 
) [inline]

Converts anisotropic displacement parameters u_cif -> beta.

Implemented as u_star_as_beta(u_cif_as_u_star(unit_cell, u_cif)).

References u_cif_as_u_star(), and u_star_as_beta().

sym_mat3<FloatType> cctbx::adptbx::u_cif_as_u_cart ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cif 
) [inline]

Converts anisotropic displacement parameters u_cif -> u_cart.

Implemented without a significant loss of efficiency as u_star_as_u_cart(unit_cell, u_cif_as_u_star(unit_cell, u_cif)).

References u_cif_as_u_star(), and u_star_as_u_cart().

Referenced by u_cif_as_u_iso().

FloatType cctbx::adptbx::u_cif_as_u_iso ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cif 
) [inline]

Converts u_cif -> u_iso.

Implemented as u_cart_as_u_iso(u_cif_as_u_cart(unit_cell, u_cif)).

References u_cart_as_u_iso(), and u_cif_as_u_cart().

sym_mat3<FloatType> cctbx::adptbx::u_cif_as_u_star ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_cif 
) [inline]

Converts anisotropic displacement parameters u_cif -> u_star.

The transformation matrix used is:

              (a*  0  0)
          c = ( 0 b*  0)
              ( 0  0 c*)
The formula for the transformation is u_star = c * u_cif * c.transpose(). In this particular case the expression simplifies to:
          u_star_11 = a*^2  u_cif_11
          u_star_22 = b*^2  u_cif_22
          u_star_33 = c*^2  u_cif_33
          u_star_12 = a* b* u_cif_12
          u_star_13 = a* c* u_cif_13
          u_star_23 = b* c* u_cif_23

References unit_cell::reciprocal_parameters().

Referenced by debye_waller_factor_u_cif(), u_cif_as_beta(), and u_cif_as_u_cart().

sym_mat3<FloatType> cctbx::adptbx::u_iso_as_beta ( uctbx::unit_cell const &  unit_cell,
FloatType const &  u_iso 
) [inline]

Converts u_iso -> beta.

Implemented as u_cart_as_beta(unit_cell, u_iso_as_u_cart(u_iso)).

References u_cart_as_beta(), and u_iso_as_u_cart().

sym_mat3<FloatType> cctbx::adptbx::u_iso_as_u_cart ( FloatType const &  u_iso  )  [inline]

Converts u_iso -> anisotropic displacement parameters u_cart.

The diagonal elements of u_cart are set to the value of u_iso. The off-diagonal components u_cart are set to zero.

Referenced by u_iso_as_beta(), u_iso_as_u_cif(), and u_iso_as_u_star().

sym_mat3<FloatType> cctbx::adptbx::u_iso_as_u_cif ( uctbx::unit_cell const &  unit_cell,
FloatType const &  u_iso 
) [inline]

Converts u_iso -> u_cif.

Implemented as u_cart_as_u_cif(unit_cell, u_iso_as_u_cart(u_iso)).

References u_cart_as_u_cif(), and u_iso_as_u_cart().

sym_mat3<FloatType> cctbx::adptbx::u_iso_as_u_star ( uctbx::unit_cell const &  unit_cell,
FloatType const &  u_iso 
) [inline]

Converts u_iso -> u_star.

Implemented as u_cart_as_u_star(unit_cell, u_iso_as_u_cart(u_iso)).

References u_cart_as_u_star(), and u_iso_as_u_cart().

Referenced by scatterer< float_type >::convert_to_anisotropic(), and scatterer< float_type >::shift_u().

sym_mat3<FloatType> cctbx::adptbx::u_star_as_beta ( sym_mat3< FloatType > const &  u_star  )  [inline]

Converts anisotropic displacement parameters u_star -> beta.

The elements of u_star are multiplied by 2pi^2.

Referenced by u_cart_as_beta(), and u_cif_as_beta().

sym_mat3<FloatType> cctbx::adptbx::u_star_as_u_cart ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_star 
) [inline]

sym_mat3<FloatType> cctbx::adptbx::u_star_as_u_cif ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_star 
) [inline]

Converts anisotropic displacement parameters u_star -> u_cif.

Inverse of u_cif_as_u_star().

References unit_cell::reciprocal_parameters().

Referenced by beta_as_u_cif(), and u_cart_as_u_cif().

FloatType cctbx::adptbx::u_star_as_u_iso ( uctbx::unit_cell const &  unit_cell,
sym_mat3< FloatType > const &  u_star 
) [inline]

Converts u_star -> u_iso.

Implemented as u_cart_as_u_iso(u_star_as_u_cart(unit_cell, u_star)).

References u_cart_as_u_iso(), and u_star_as_u_cart().

Referenced by scatterer< float_type >::convert_to_isotropic(), and scatterer< float_type >::u_iso_or_equiv().


Generated on Thu Jun 19 15:34:55 2014 for cctbx by  doxygen 1.5.6