rotation_derivative Struct Reference

Helper class for calculating the derivative of rotation. More...

#include <colvar_rotation_derivative.h>

Inheritance diagram for rotation_derivative:

Collaboration diagram for rotation_derivative:

Public Member Functions
	rotation_derivative (const cvm::rotation &rot, const std::vector< cvm::real > &pos1, const std::vector< cvm::real > &pos2, const size_t num_atoms_pos1, const size_t num_atoms_pos2)
	Constructor of the cvm::rotation::derivative class for SOA. More...
void	prepare_derivative (rotation_derivative_dldq require_dl_dq)
	This function must be called before calc_derivative_wrt_group1 and calc_derivative_wrt_group2 in order to prepare the tmp_Q0Q0 and tmp_Q0Q0_L. More...
template<bool use_dl, bool use_dq, bool use_ds>
void	calc_derivative_impl (const cvm::rvector(&ds)[4][4], cvm::rvector *_noalias const dl0_out, cvm::vector1d< cvm::rvector > *_noalias const dq0_out, cvm::matrix2d< cvm::rvector > *_noalias const ds_out) const
	Actual implementation of the derivative calculation. More...
template<bool use_dl, bool use_dq, bool use_ds>
void	calc_derivative_wrt_group1 (size_t ia, cvm::rvector *_noalias const dl0_1_out=nullptr, cvm::vector1d< cvm::rvector > *_noalias const dq0_1_out=nullptr, cvm::matrix2d< cvm::rvector > *_noalias const ds_1_out=nullptr) const
	Calculate the derivatives of S, the leading eigenvalue L and the leading eigenvector Q with respect to m_pos1 More...
template<bool use_dl, bool use_dq, bool use_ds>
void	calc_derivative_wrt_group2 (size_t ia, cvm::rvector *_noalias const dl0_2_out=nullptr, cvm::vector1d< cvm::rvector > *_noalias const dq0_2_out=nullptr, cvm::matrix2d< cvm::rvector > *_noalias const ds_2_out=nullptr) const
	Calculate the derivatives of S, the leading eigenvalue L and the leading eigenvector Q with respect to m_pos2 More...

Public Attributes
const cvm::rotation &	m_rot
	Reference to the rotation.
const std::vector< cvm::real > &	m_pos1
	Reference to the atom positions of group 1.
const std::vector< cvm::real > &	m_pos2
	Reference to the atom positions of group 2.
size_t	m_num_atoms_pos1
	Number of atoms in group1 (used in SOA)
size_t	m_num_atoms_pos2
	Number of atoms in group1 (used in SOA)
cvm::real	tmp_Q0Q0 [4][4]
	Temporary variable that will be updated if prepare_derivative called.
cvm::real	tmp_Q0Q0_L [4][4][4]

Detailed Description

Helper class for calculating the derivative of rotation.

Constructor & Destructor Documentation

rotation_derivative()

rotation_derivative::rotation_derivative ( const cvm::rotation &  rot, const std::vector< cvm::real > &  pos1, const std::vector< cvm::real > &  pos2, const size_t  num_atoms_pos1, const size_t  num_atoms_pos2  )

inline

Constructor of the cvm::rotation::derivative class for SOA.

Parameters

[in]	rot	The cvm::rotation object (must have called calc_optimal_rotation before calling calc_derivative_wrt_group1 and calc_derivative_wrt_group2)
[in]	pos1	The atom positions of group 1
[in]	pos2	The atom positions of group 2
[in]	num_atoms_pos1	The number of atoms in group1
[in]	num_atoms_pos2	The number of atoms in group2

Member Function Documentation

calc_derivative_impl()

template<bool use_dl, bool use_dq, bool use_ds>

void rotation_derivative::calc_derivative_impl ( const cvm::rvector(&)  ds[4][4], cvm::rvector *_noalias const  dl0_out, cvm::vector1d< cvm::rvector > *_noalias const  dq0_out, cvm::matrix2d< cvm::rvector > *_noalias const  ds_out  ) const

inline

Actual implementation of the derivative calculation.

Parameters

[in]	ds	The derivative of matrix S with respect to an atom of either group 1 or group 2
[out]	dl0_out	The output of derivative of L
[out]	dq0_out	The output of derivative of Q
[out]	ds_out	The output of derivative of overlap matrix S

calc_derivative_wrt_group1()

template<bool use_dl, bool use_dq, bool use_ds>

void rotation_derivative::calc_derivative_wrt_group1 ( size_t  ia, cvm::rvector *_noalias const  dl0_1_out = nullptr, cvm::vector1d< cvm::rvector > *_noalias const  dq0_1_out = nullptr, cvm::matrix2d< cvm::rvector > *_noalias const  ds_1_out = nullptr  ) const

inline

Calculate the derivatives of S, the leading eigenvalue L and the leading eigenvector Q with respect to m_pos1

Parameters

[in]	ia	The index the of atom
[out]	dl0_1_out	The output of derivative of L with respect to ia-th atom of group 1
[out]	dq0_1_out	The output of derivative of Q with respect to ia-th atom of group 1
[out]	ds_1_out	The output of derivative of overlap matrix S with respect to ia-th atom of group 1

calc_derivative_wrt_group2()

template<bool use_dl, bool use_dq, bool use_ds>

void rotation_derivative::calc_derivative_wrt_group2 ( size_t  ia, cvm::rvector *_noalias const  dl0_2_out = nullptr, cvm::vector1d< cvm::rvector > *_noalias const  dq0_2_out = nullptr, cvm::matrix2d< cvm::rvector > *_noalias const  ds_2_out = nullptr  ) const

inline

Calculate the derivatives of S, the leading eigenvalue L and the leading eigenvector Q with respect to m_pos2

Parameters

[in]	ia	The index the of atom
[out]	dl0_2_out	The output of derivative of L with respect to ia-th atom of group 2
[out]	dq0_2_out	The output of derivative of Q with respect to ia-th atom of group 2
[out]	ds_2_out	The output of derivative of overlap matrix S with respect to ia-th atom of group 2

prepare_derivative()

void rotation_derivative::prepare_derivative ( rotation_derivative_dldq  require_dl_dq )

inline

This function must be called before calc_derivative_wrt_group1 and calc_derivative_wrt_group2 in order to prepare the tmp_Q0Q0 and tmp_Q0Q0_L.

Parameters

[in]

require_dl_dq

Require the calculation of the derivatives of L or/and Q with respect to atoms.

---

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

• colvar_rotation_derivative.h