A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion) More...
#include <colvartypes.h>
Collaboration diagram for colvarmodule::rotation:
Public Member Functions | |
| void | request_group1_gradients (size_t n) |
| Allocate space for the derivatives of the rotation. | |
| void | request_group2_gradients (size_t n) |
| Allocate space for the derivatives of the rotation. | |
| void | calc_optimal_rotation (std::vector< atom_pos > const &pos1, std::vector< atom_pos > const &pos2) |
| Calculate the optimal rotation and store the corresponding eigenvalue and eigenvector in the arguments l0 and q0; if the gradients have been previously requested, calculate them as well. More... | |
| int | init () |
| Initialize member data. | |
| rotation () | |
| Default constructor. | |
| rotation (cvm::quaternion const &qi) | |
| Constructor after a quaternion. | |
| rotation (cvm::real angle, cvm::rvector const &axis) | |
| Constructor after an axis of rotation and an angle (in radians) | |
| ~rotation () | |
| Destructor. | |
| cvm::rvector | rotate (cvm::rvector const &v) const |
| Return the rotated vector. | |
| cvm::rotation | inverse () const |
| Return the inverse of this rotation. | |
| cvm::rmatrix | matrix () const |
| Return the associated 3x3 matrix. | |
| cvm::real | spin_angle (cvm::rvector const &axis) const |
| Return the spin angle (in degrees) with respect to the provided axis (which MUST be normalized) | |
| cvm::quaternion | dspin_angle_dq (cvm::rvector const &axis) const |
| Return the derivative of the spin angle with respect to the quaternion. | |
| cvm::real | cos_theta (cvm::rvector const &axis) const |
| Return the projection of the orientation vector onto a predefined axis. | |
| cvm::quaternion | dcos_theta_dq (cvm::rvector const &axis) const |
| Return the derivative of the tilt wrt the quaternion. | |
Public Attributes | |
| cvm::quaternion | q |
| The rotation itself (implemented as a quaternion) | |
| cvm::real | lambda |
| Eigenvalue corresponding to the optimal rotation. | |
| bool | b_debug_gradients |
| Perform gradient tests. | |
| cvm::rmatrix | C |
| Correlation matrix C (3, 3) | |
| cvm::matrix2d< cvm::real > | S |
| Overlap matrix S (4, 4) | |
| cvm::vector1d< cvm::real > | S_eigval |
| Eigenvalues of S. | |
| cvm::matrix2d< cvm::real > | S_eigvec |
| Eigenvectors of S. | |
| cvm::matrix2d< cvm::real > | S_backup |
| Used for debugging gradients. | |
| std::vector< cvm::matrix2d< cvm::rvector > > | dS_1 |
| Derivatives of S. | |
| std::vector< cvm::matrix2d< cvm::rvector > > | dS_2 |
| std::vector< cvm::rvector > | dL0_1 |
| Derivatives of leading eigenvalue. | |
| std::vector< cvm::rvector > | dL0_2 |
| std::vector< cvm::vector1d< cvm::rvector > > | dQ0_1 |
| Derivatives of leading eigenvector. | |
| std::vector< cvm::vector1d< cvm::rvector > > | dQ0_2 |
Static Public Attributes | |
| static bool | monitor_crossings = false |
| Whether to test for eigenvalue crossing. | |
| static cvm::real | crossing_threshold = 1.0E-02 |
| Threshold for the eigenvalue crossing test. | |
Protected Member Functions | |
| void | build_correlation_matrix (std::vector< cvm::atom_pos > const &pos1, std::vector< cvm::atom_pos > const &pos2) |
| Build the correlation matrix C (used by calc_optimal_rotation()) | |
| void | compute_overlap_matrix () |
| Compute the overlap matrix S (used by calc_optimal_rotation()) | |
Protected Attributes | |
| cvm::quaternion | q_old |
| Previous value of the rotation (used to warn the user when the structure changes too much, and there may be an eigenvalue crossing) | |
| void * | jacobi |
| Pointer to instance of Jacobi solver. | |
Detailed Description
A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)
Member Function Documentation
◆ calc_optimal_rotation()
| void colvarmodule::rotation::calc_optimal_rotation | ( | std::vector< atom_pos > const & | pos1, |
| std::vector< atom_pos > const & | pos2 | ||
| ) |
Calculate the optimal rotation and store the corresponding eigenvalue and eigenvector in the arguments l0 and q0; if the gradients have been previously requested, calculate them as well.
The method to derive the optimal rotation is defined in: Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254
The documentation for this class was generated from the following files:
- colvartypes.h
- colvartypes.cpp
