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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 >

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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.

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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.

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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.

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

• colvar_geometricpath.h

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