Complete documentation¶

d_vector¶

This class creates and manages an array on the device (aka. on the GPU).

Properties¶

int

length

The length of the array. It cannot be resized.

Methods¶

d_vector(int n)¶

The constructor creates an array of size n on the device.

float at(int i)¶

Returns the i’th element of the array.

float dot(d_vector other)¶

Returns the dot product of this d_vector and the other d_vector.

d_spmatrix¶

This class creates and manages a sparse matrix the device (aka. on the GPU).

Properties¶

(int, int)	shape	A (rows, columns) tuple representing the shape of the matrix.
int	nnz	Number of non-zero elements in the matrix.
matrix_type	dtype	Number of non-zero elements in the matrix.

Methods¶

d_spmatrix(int rows, int columns, int nnz = 0, matrix_type type = COO)¶

The constructor creates a sparse matrix of shape (rows, columns) with nnz non-zero elements on the device.

void to_csr()¶

Converts a COO matrix into a CSR matrix.

matrix_type¶

An enum that represents the data storage type of a sparse matrix.

Values¶

0	COO
1	CSR
2	CSC

state¶

A class for managing the concentrations of species. A state will create and hold a d_vector for each species you add.

Properties¶

int	n_species	Number of species
int	vector_size	Number of spatial nodes for each species

Methods¶

state (int vector_size)¶

The constructor creates a state that will hold vector_size sized species.

add_species (string name, bool diffusion = true)¶

Add a species called name to the state. Set diffusion to False if you don’t want the species to be affected by diffusion.

d_vector get_species (string name)¶

Returns a reference to the current vector of the given species.

Returns NULL if the species is not found.

void set_species (string name, d_vector species_vector)¶

Copies the given vector as the new state-vector of the given species.

If the species is not found, it does nothing.

void set_species (string name, numpy.array species_vector)¶

Overloads the above method.

You can specify the vector as numpy array.

void print (int printCount = 5)¶

Prints each species and its vector.

For each vector, only printCount elements will be printed.

void list_species ()¶

Returns the species of the state as a list of strings.

simulation¶

A class for managing simulations. A simulation will create and hold a state.

Properties¶

state	current_state	The state object held by the simulation
float	epsilon	The error of the conjugate gradient method. Defaults at 10e-3
float	drain	The drain is a constant value that is deducted from the concentration of each species after each reaction-step

Methods¶

simulation (int vector_size)¶

The constructor creates a simulation and a state that holds vector_size sized species.

add_species (string name, bool diffusion = true)¶

Add a species called name to the current_state. Set diffusion to False if you don’t want the species to be affected by diffusion.

d_vector get_species (string name)¶

Returns a reference to the current vector of the given species.

Returns NULL if the species is not found.

void set_species (string name, d_vector species_vector)¶

Copies the given vector as the new state-vector of the given species.

If the species is not found, it does nothing.

void set_species (string name, numpy.array species_vector)¶

Overloads the above method.

You can specify the vector as numpy array.

void add_reaction (string reaction, float rate)¶

Adds the given reaction to the simulation. It will be taken into account in all future reaction-steps.

Some examples of reactions that can be written:

"A + B -> C"

" B+C-> "

Note that this method will raise an error if any of the mentioned species has not be added beforehand.

void add_reversible_reaction (string reaction, float rate_forward, float rate_back)¶

Similar to the add_reaction method. Adds both the given reaction and its reverse. The rates for each of the two reactions has to be specified.

void load_dampness_matrix (d_spmatrix dampness_matrix)¶

Sets the given matrix as the reactor’s dampness matrix. Mandatory for performing diffusion.

void load_stiffness_matrix (d_spmatrix stiffness_matrix)¶

Sets the given matrix as the reactor’s stiffness matrix. Mandatory for performing diffusion.