bridgeObjects.cc File Reference

Solves the triaxial loop closure problem for a system of atoms. More...

#include <cmath>
#include <utility/vector1.hh>
#include <utility/fixedsizearray1.hh>
#include <numeric/types.hh>
#include <numeric/kinematic_closure/dixon.hh>
#include <numeric/kinematic_closure/kinematic_closure_helpers.hh>
#include <iostream>

Namespaces
	numeric
	Unit headers.
	numeric::kinematic_closure

Macros
#define	rad2deg   57.2957795130823208767981548141051703
#define	deg2rad   0.0174532925199432957692369076848861271
#define	pi   3.14159265358979323846264338327950288
#define	pidegs   180.0

Functions
void	numeric::kinematic_closure::triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 3 > &calpha, utility::fixedsizearray1< Real, 3 > &salpha)
void	numeric::kinematic_closure::triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 4 > &calpha, utility::fixedsizearray1< Real, 4 > &salpha)
void	numeric::kinematic_closure::sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 3 > &cosine, utility::fixedsizearray1< Real, 3 > &sine)
void	numeric::kinematic_closure::sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 4 > &cosine, utility::fixedsizearray1< Real, 4 > &sine)
void	numeric::kinematic_closure::triaxialCoefficients (const utility::fixedsizearray1< Real, 3 > &vb, const utility::fixedsizearray1< Real, 3 > &xi, const utility::fixedsizearray1< Real, 3 > &eta, const utility::fixedsizearray1< Real, 3 > &delta, const utility::fixedsizearray1< Real, 3 > &theta, const utility::vector1< int > &order, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &A, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &B, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &C, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &D, utility::fixedsizearray1< Real, 3 > &cal, utility::fixedsizearray1< Real, 3 > &sal, int &f)
void	numeric::kinematic_closure::cross (const utility::fixedsizearray1< Real, 3 > &L, const utility::fixedsizearray1< Real, 3 > &r0, utility::fixedsizearray1< Real, 3 > &r)
void	numeric::kinematic_closure::frame (const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &R, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &U)
Real	numeric::kinematic_closure::eucDistance (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b)
Real	numeric::kinematic_closure::scpn (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)
Real	numeric::kinematic_closure::bondangle (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)
Real	numeric::kinematic_closure::torsion (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c, const utility::fixedsizearray1< Real, 3 > &d)
void	numeric::kinematic_closure::chainParams (const int &n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, Real &vbond, Real &xi, Real &eta, Real &delta, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)
void	numeric::kinematic_closure::chainXYZ (const int &n, const utility::vector1< Real > &b_len1, const utility::vector1< Real > &b_ang1, const utility::vector1< Real > &t_ang1, const bool space, const utility::fixedsizearray1< Real, 3 > &R0, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &Q, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)
void	numeric::kinematic_closure::chainXYZ (const int &n, const utility::vector1< Real > &b_len, const utility::vector1< Real > &b_ang, const utility::vector1< Real > &t_ang, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)
void	numeric::kinematic_closure::chainTORS (const int &n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, utility::vector1< Real > &t_ang, utility::vector1< Real > &b_ang, utility::vector1< Real > &b_len, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)
void	numeric::kinematic_closure::rotateX (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rx)
void	numeric::kinematic_closure::rotateY (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Ry)
void	numeric::kinematic_closure::rotateZ (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rz)
void	numeric::kinematic_closure::bridgeObjects (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, const utility::vector1< Real > &dt, const utility::vector1< Real > &da, const utility::vector1< Real > &db, const utility::vector1< int > &pivots, const utility::vector1< int > &order, utility::vector1< utility::vector1< Real > > &t_ang, utility::vector1< utility::vector1< Real > > &b_ang, utility::vector1< utility::vector1< Real > > &b_len, int &nsol)
	Solve the triaxial loop closure problem for a system of atoms. More...
void	numeric::kinematic_closure::test_bridgeObjects ()
void	numeric::kinematic_closure::test_rotateX ()
void	numeric::kinematic_closure::test_chainTORS ()
void	numeric::kinematic_closure::test_chainXYZ ()
void	numeric::kinematic_closure::test_chainParams ()
void	numeric::kinematic_closure::test_torsion ()
void	numeric::kinematic_closure::test_bondangle ()
void	numeric::kinematic_closure::test_scpn ()
void	numeric::kinematic_closure::test_eucDistance ()
void	numeric::kinematic_closure::test_frame ()
void	numeric::kinematic_closure::test_cross ()
void	numeric::kinematic_closure::test_triaxialCoefficients ()
void	numeric::kinematic_closure::test_sincos ()
void	numeric::kinematic_closure::test_triangle ()

Detailed Description

Solves the triaxial loop closure problem for a system of atoms.

Author

Evangelos A. Coutsias

Daniel J. Mandell

Macro Definition Documentation

#define deg2rad   0.0174532925199432957692369076848861271

Referenced by numeric::kinematic_closure::bridgeObjects(), and numeric::kinematic_closure::chainXYZ().

#define pi   3.14159265358979323846264338327950288

Referenced by numeric::UniformRotationSampler::generateIcosahedralSamples(), numeric::fourier::kiss_fft_state::kiss_fft_state(), numeric::fourier::kiss_fft_state::resize(), shift_angles(), numeric::UniformRotationSampler::UniformRotationSampler(), and numeric::statistics::w().

#define pidegs   180.0

Referenced by numeric::kinematic_closure::torsion().

#define rad2deg   57.2957795130823208767981548141051703

Referenced by numeric::kinematic_closure::bondangle(), and numeric::kinematic_closure::torsion().