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GeometricPathCV::GeometricPathBase Class Template Reference

#include <colvar_geometricpath.h>

List of all members.

Public Methods

 GeometricPathBase (size_t vector_size, const element_type &element=element_type(), size_t total_frames=1, bool p_use_second_closest_frame=true, bool p_use_third_closest_frame=false, bool p_use_z_square=false)
 GeometricPathBase (size_t vector_size, const std::vector< element_type > &elements, size_t total_frames=1, bool p_use_second_closest_frame=true, bool p_use_third_closest_frame=false, bool p_use_z_square=false)
 GeometricPathBase ()
virtual ~GeometricPathBase ()
virtual void initialize (size_t vector_size, const element_type &element=element_type(), size_t total_frames=1, bool p_use_second_closest_frame=true, bool p_use_third_closest_frame=false, bool p_use_z_square=false)
virtual void initialize (size_t vector_size, const std::vector< element_type > &elements, size_t total_frames=1, bool p_use_second_closest_frame=true, bool p_use_third_closest_frame=false, bool p_use_z_square=false)
virtual void prepareVectors ()=0
virtual void updateDistanceToReferenceFrames ()=0
virtual void compute ()
virtual void determineClosestFrames ()
virtual void computeValue ()
virtual void computeDerivatives ()

Protected Attributes

scalar_type v1v1
scalar_type v2v2
scalar_type v3v3
scalar_type v4v4
scalar_type v1v3
scalar_type v1v4
scalar_type f
scalar_type dx
scalar_type s
scalar_type z
scalar_type zz
std::vector< element_type > v1
std::vector< element_type > v2
std::vector< element_type > v3
std::vector< element_type > v4
std::vector< element_type > dfdv1
std::vector< element_type > dfdv2
std::vector< element_type > dzdv1
std::vector< element_type > dzdv2
std::vector< scalar_type > frame_distances
std::vector< size_t > frame_index
bool use_second_closest_frame
bool use_third_closest_frame
bool use_z_square
long min_frame_index_1
long min_frame_index_2
long min_frame_index_3
long sign
double M
double m

template<typename element_type, typename scalar_type, path_sz path_type>
class GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >


Constructor & Destructor Documentation

template<typename element_type, typename scalar_type, path_sz path_type>
GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::GeometricPathBase size_t    vector_size,
const element_type &    element = element_type(),
size_t    total_frames = 1,
bool    p_use_second_closest_frame = true,
bool    p_use_third_closest_frame = false,
bool    p_use_z_square = false
 

Definition at line 79 of file colvar_geometricpath.h.

References initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::GeometricPathBase size_t    vector_size,
const std::vector< element_type > &    elements,
size_t    total_frames = 1,
bool    p_use_second_closest_frame = true,
bool    p_use_third_closest_frame = false,
bool    p_use_z_square = false
 

Definition at line 84 of file colvar_geometricpath.h.

References initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::GeometricPathBase   [inline]
 

Definition at line 66 of file colvar_geometricpath.h.

template<typename element_type, typename scalar_type, path_sz path_type>
virtual GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::~GeometricPathBase   [inline, virtual]
 

Definition at line 67 of file colvar_geometricpath.h.


Member Function Documentation

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::compute   [virtual]
 

Definition at line 155 of file colvar_geometricpath.h.

References computeDerivatives, and computeValue.

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::computeDerivatives   [virtual]
 

Definition at line 225 of file colvar_geometricpath.h.

References dfdv1, dfdv2, dzdv1, dzdv2, f, colvarmodule::sqrt, v1, v1v1, v1v3, v1v4, v2, v2v2, v3, v3v3, v4, v4v4, z, and GeometricPathCV::Z.

Referenced by compute.

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::computeValue   [virtual]
 

Definition at line 187 of file colvar_geometricpath.h.

References determineClosestFrames, dx, f, M, m, prepareVectors, s, GeometricPathCV::S, colvarmodule::sqrt, updateDistanceToReferenceFrames, v1, v1v1, v1v3, v1v4, v2, v2v2, v3, v3v3, v4, v4v4, z, GeometricPathCV::Z, and zz.

Referenced by compute.

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::determineClosestFrames   [virtual]
 

Definition at line 161 of file colvar_geometricpath.h.

References colvarmodule::fabs, frame_distances, frame_index, m, min_frame_index_1, min_frame_index_2, min_frame_index_3, sign, use_second_closest_frame, and use_third_closest_frame.

Referenced by computeValue.

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::initialize size_t    vector_size,
const std::vector< element_type > &    elements,
size_t    total_frames = 1,
bool    p_use_second_closest_frame = true,
bool    p_use_third_closest_frame = false,
bool    p_use_z_square = false
[virtual]
 

Definition at line 122 of file colvar_geometricpath.h.

References dfdv1, dfdv2, dx, dzdv1, dzdv2, f, frame_distances, frame_index, m, M, sign, use_second_closest_frame, use_third_closest_frame, use_z_square, v1, v1v1, v1v3, v1v4, v2, v2v2, v3, v3v3, v4, v4v4, z, and zz.

template<typename element_type, typename scalar_type, path_sz path_type>
void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::initialize size_t    vector_size,
const element_type &    element = element_type(),
size_t    total_frames = 1,
bool    p_use_second_closest_frame = true,
bool    p_use_third_closest_frame = false,
bool    p_use_z_square = false
[virtual]
 

Definition at line 89 of file colvar_geometricpath.h.

References dfdv1, dfdv2, dx, dzdv1, dzdv2, f, frame_distances, frame_index, m, M, sign, use_second_closest_frame, use_third_closest_frame, use_z_square, v1, v1v1, v1v3, v1v4, v2, v2v2, v3, v3v3, v4, v4v4, z, and zz.

Referenced by GeometricPathBase.

template<typename element_type, typename scalar_type, path_sz path_type>
virtual void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::prepareVectors   [pure virtual]
 

Referenced by computeValue.

template<typename element_type, typename scalar_type, path_sz path_type>
virtual void GeometricPathCV::GeometricPathBase< element_type, scalar_type, path_type >::updateDistanceToReferenceFrames   [pure virtual]
 

Referenced by computeValue.


Member Data Documentation

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::dfdv1 [protected]
 

Definition at line 48 of file colvar_geometricpath.h.

Referenced by computeDerivatives, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::dfdv2 [protected]
 

Definition at line 49 of file colvar_geometricpath.h.

Referenced by computeDerivatives, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::dx [protected]
 

Definition at line 40 of file colvar_geometricpath.h.

Referenced by computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::dzdv1 [protected]
 

Definition at line 50 of file colvar_geometricpath.h.

Referenced by computeDerivatives, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::dzdv2 [protected]
 

Definition at line 51 of file colvar_geometricpath.h.

Referenced by computeDerivatives, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::f [protected]
 

Definition at line 39 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<scalar_type> GeometricPathCV::GeometricPathBase::frame_distances [protected]
 

Definition at line 52 of file colvar_geometricpath.h.

Referenced by determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<size_t> GeometricPathCV::GeometricPathBase::frame_index [protected]
 

Definition at line 53 of file colvar_geometricpath.h.

Referenced by determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
double GeometricPathCV::GeometricPathBase::m [protected]
 

Definition at line 62 of file colvar_geometricpath.h.

Referenced by computeValue, determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
double GeometricPathCV::GeometricPathBase::M [protected]
 

Definition at line 61 of file colvar_geometricpath.h.

Referenced by computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
long GeometricPathCV::GeometricPathBase::min_frame_index_1 [protected]
 

Definition at line 57 of file colvar_geometricpath.h.

Referenced by determineClosestFrames.

template<typename element_type, typename scalar_type, path_sz path_type>
long GeometricPathCV::GeometricPathBase::min_frame_index_2 [protected]
 

Definition at line 58 of file colvar_geometricpath.h.

Referenced by determineClosestFrames.

template<typename element_type, typename scalar_type, path_sz path_type>
long GeometricPathCV::GeometricPathBase::min_frame_index_3 [protected]
 

Definition at line 59 of file colvar_geometricpath.h.

Referenced by determineClosestFrames.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::s [protected]
 

Definition at line 41 of file colvar_geometricpath.h.

Referenced by computeValue.

template<typename element_type, typename scalar_type, path_sz path_type>
long GeometricPathCV::GeometricPathBase::sign [protected]
 

Definition at line 60 of file colvar_geometricpath.h.

Referenced by determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
bool GeometricPathCV::GeometricPathBase::use_second_closest_frame [protected]
 

Definition at line 54 of file colvar_geometricpath.h.

Referenced by determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
bool GeometricPathCV::GeometricPathBase::use_third_closest_frame [protected]
 

Definition at line 55 of file colvar_geometricpath.h.

Referenced by determineClosestFrames, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
bool GeometricPathCV::GeometricPathBase::use_z_square [protected]
 

Definition at line 56 of file colvar_geometricpath.h.

Referenced by initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::v1 [protected]
 

Definition at line 44 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v1v1 [protected]
 

Definition at line 33 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v1v3 [protected]
 

Definition at line 37 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v1v4 [protected]
 

Definition at line 38 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::v2 [protected]
 

Definition at line 45 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v2v2 [protected]
 

Definition at line 34 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::v3 [protected]
 

Definition at line 46 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v3v3 [protected]
 

Definition at line 35 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
std::vector<element_type> GeometricPathCV::GeometricPathBase::v4 [protected]
 

Definition at line 47 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::v4v4 [protected]
 

Definition at line 36 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::z [protected]
 

Definition at line 42 of file colvar_geometricpath.h.

Referenced by computeDerivatives, computeValue, and initialize.

template<typename element_type, typename scalar_type, path_sz path_type>
scalar_type GeometricPathCV::GeometricPathBase::zz [protected]
 

Definition at line 43 of file colvar_geometricpath.h.

Referenced by computeValue, and initialize.


The documentation for this class was generated from the following file:
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