colvars_gpu::rotation_gpu Class Reference

Collaboration diagram for colvars_gpu::rotation_gpu:

Public Member Functions
	rotation_gpu ()
	Constructor.
	~rotation_gpu ()
	Destructor.
bool	initialized () const
	Check if the object is initialized.
int	init ()
	Initialize member data.
int	add_optimal_rotation_nodes (cvm::real *const d_pos1, cvm::real *const d_pos2, const size_t num_atoms_pos1, const size_t num_atoms_pos2, cudaGraph_t &graph, std::unordered_map< std::string, cudaGraphNode_t > &nodes_map)
	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.
void	check_error () const
	Checking after synchronization ( eigendecomposition iterations and max crossing).
cvm::real *	get_S () const
cvm::real *	get_eigenvectors () const
cvm::real *	get_eigenvalues () const
cvm::quaternion *	get_q () const
void	to_cpu (cvm::rotation &rot) const

Private Attributes
cvm::real *	d_S
	Correlation matrix C (3, 3).
cvm::real *	d_S_eigval
	Eigenvalues of S.
cvm::real *	d_S_eigvec
	Eigenvectors of S.
unsigned int *	tbcount
	Used for debugging gradients.
cvm::quaternion *	d_q
	The rotation itself (implemented as a quaternion).
cvm::quaternion *	d_q_old
	Crossing monitor.
int *	discontinuous_rotation
int *	max_iteration_reached
	Flag for checking if eigendecomposition is failed.
bool	b_initialized
	Flag for checking if initialized.
cvm::rmatrix *	h_C
	Host data for compatibility with CPU buffers.
cvm::real *	h_S
cvm::real *	h_S_eigval
cvm::real *	h_S_eigvec
cudaEvent_t	jacobi_done
	CUDA event for checking if max iterations are reached.

Friends
struct	rotation_derivative_gpu

Member Function Documentation

add_optimal_rotation_nodes()

int colvars_gpu::rotation_gpu::add_optimal_rotation_nodes	(	cvm::real *const	d_pos1,
		cvm::real *const	d_pos2,
		const size_t	num_atoms_pos1,
		const size_t	num_atoms_pos2,
		cudaGraph_t &	graph,
		std::unordered_map< std::string, cudaGraphNode_t > &	nodes_map )

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

Member Data Documentation

d_S

cvm::real* colvars_gpu::rotation_gpu::d_S

private

Correlation matrix C (3, 3).

Overlap matrix S (4, 4)

d_S_eigvec

cvm::real* colvars_gpu::rotation_gpu::d_S_eigvec

private

Eigenvectors of S.

Note

d_S_eigvec is in column-major order. To get j-th element of the i-th eigenvector, use d_S_eigvec[i*4+j]

tbcount

unsigned int* colvars_gpu::rotation_gpu::tbcount

private

Used for debugging gradients.

Eigensolver Thread block atomic counter

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

• colvartypes.h
• colvartypes.cpp