Holds data needed by each CUDA thread to execute its work. More...

Public Member Functions
__device__ void	solution_from_directions (int3 solution, char directions)
	Given a vector of relative directions, returns a vector of coordinates generated by these directions. More...

__device__ void	local_search (int &solContact, int lsFreq)
	Performs local search in the thread's own solution, replacing `mySolution` if a better solution is found. More...

__device__ double &	pheromone (int i, int d)
	Getter for individual pheromones. More...

__device__ int	calculate_contacts (int3 *solution)
	Counts contacts within the given solution. More...

__device__ void	get_heuristics (int curSize, int3 solution, double heurs, int3 *possiblePos)
	Calculates the heuristic value for the step being decided. More...

__device__ void	get_probabilities (int movIndex, double probs, double heurs)
	Calculates probability of following each of the 5 directions. More...

__device__ void	develop_solution (int3 solution, char directions)
	Simulates the behavior of an ant walking through the pheromone matrix, developing a solution. More...

Static Public Member Functions
static __device__ int3	DIRECTION_VECTOR (int3 prevDir, char dir)
	Returns the vector obtained by following the vector 'prevDir' and turning to direction 'dir'. More...

Public Attributes
int	tid
	Unique identifier for the thread within all blocks (the grid). More...

int	randNumber
	Random number that also serves as the seed for generation. More...

int3 *	mySolution
	Memory region containing coordinates of the solution this thread is developing. More...

int3 *	myOtherSolution
	Memory region that the thread uses for performing local seach (small perturbation) on mySolution. More...

char *	myDirections
	Memory containing relative directions for mySolution. More...

char *	myOtherDirections
	Memory containing relative directions for myOtherSolution. More...

double *	pheromones
	Pointer to the pheromone matrix (shared by all threads). More...

char *	hpChain
	hpChain of the protein being predicted (shared by all threads). More...

int	nCoords
	Number of coordinates of the protein. More...

int	nMovElems
	Number of directions of the protein. More...

double	dAlpha
	Alpha parameter of the ACO algorithm. More...

double	dBeta
	Beta parameter of the ACO algorithm. More...

Detailed Description

Holds data needed by each CUDA thread to execute its work.

We associate device functions with this structure, which makes access to this struct's data by a thread much easier.

Member Function Documentation

◆ calculate_contacts()

__device__ int CUDAThread::calculate_contacts ( int3 * solution )

Counts contacts within the given solution.

Returns: Number of contacts within the given solution, or -1 if the solution is invalid, that is, it contains a collision.

◆ develop_solution()

__device__ void CUDAThread::develop_solution	(	int3 *	solution,
		char *	directions
	)

Simulates the behavior of an ant walking through the pheromone matrix, developing a solution.

Parameters

[out]	solution	Output memory region in which to store the solution coordinates.
[out]	directions	Output memory region in which to store the solution directions.

◆ DIRECTION_VECTOR()

__device__ int3 CUDAThread::DIRECTION_VECTOR	(	int3	prevDir,
		char	dir
	)

static

Returns the vector obtained by following the vector 'prevDir' and turning to direction 'dir'.

◆ get_heuristics()

__device__ void CUDAThread::get_heuristics	(	int	curSize,
		int3 *	solution,
		double *	heurs,
		int3 *	possiblePos
	)

Calculates the heuristic value for the step being decided.

Parameters

	curSize	Number of coordinates that have already been decided. should correspond to the number of valid coordinates in the given `solution`.
	solution	Memory region containing the coordinates being decided.
[out]	heurs	Output array of 5 doubles where we store heuristic values for each direction.
	possiblePos	Array of the 5 possible positions that result by following each of the 5 directions in the current `solution`.

◆ get_probabilities()

__device__ void CUDAThread::get_probabilities	(	int	movIndex,
		double *	probs,
		double *	heurs
	)

Calculates probability of following each of the 5 directions.

Parameters

	movIndex	Index of the direction being decided.
[out]	probs	Output array with 5 doubles where we store the probability of following each of the 5 directions.
	heurs	Array with the 5 heuristic values of each possible direction.

◆ local_search()

__device__ void CUDAThread::local_search	(	int &	solContact,
		int	lsFreq
	)

Performs local search in the thread's own solution, replacing mySolution if a better solution is found.

Parameters

[out]	solContact	Output argument where we store the highest number of contacts found.
	lsFreq	Local search frequency, which defines the number of perturbations to generate.

◆ pheromone()

__device__ double & CUDAThread::pheromone	(	int	i,
		int	d
	)

Getter for individual pheromones.

Parameters

i	The index of relative direction that is currently being decided.
d	The relative direction in [0-4] that is being considered.

◆ solution_from_directions()

__device__ void CUDAThread::solution_from_directions	(	int3 *	solution,
		char *	directions
	)

Given a vector of relative directions, returns a vector of coordinates generated by these directions.

Parameters

solution	Memory region where we should store the resulting solution.
directions	Memory region containing the directions.

Member Data Documentation

◆ dAlpha

double CUDAThread::dAlpha

Alpha parameter of the ACO algorithm.

◆ dBeta

double CUDAThread::dBeta

Beta parameter of the ACO algorithm.

◆ hpChain

char* CUDAThread::hpChain

hpChain of the protein being predicted (shared by all threads).

◆ myDirections

char* CUDAThread::myDirections

Memory containing relative directions for mySolution.

◆ myOtherDirections

char* CUDAThread::myOtherDirections

Memory containing relative directions for myOtherSolution.

◆ myOtherSolution

int3* CUDAThread::myOtherSolution

Memory region that the thread uses for performing local seach (small perturbation) on mySolution.

◆ mySolution

int3* CUDAThread::mySolution

Memory region containing coordinates of the solution this thread is developing.

◆ nCoords

int CUDAThread::nCoords

Number of coordinates of the protein.

◆ nMovElems

int CUDAThread::nMovElems

Number of directions of the protein.

◆ pheromones

double* CUDAThread::pheromones

Pointer to the pheromone matrix (shared by all threads).

◆ randNumber

int CUDAThread::randNumber

Random number that also serves as the seed for generation.

◆ tid

int CUDAThread::tid

Unique identifier for the thread within all blocks (the grid).

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

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ calculate_contacts()

◆ develop_solution()

◆ DIRECTION_VECTOR()

◆ get_heuristics()

◆ get_probabilities()

◆ local_search()

◆ pheromone()

◆ solution_from_directions()

Member Data Documentation

◆ dAlpha

◆ dBeta

◆ hpChain

◆ myDirections

◆ myOtherDirections

◆ myOtherSolution

◆ mySolution

◆ nCoords

◆ nMovElems

◆ pheromones

◆ randNumber

◆ tid