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Macros
#define	BUFFER_SIZE 10

#define	SMALL_NUMBER 1e-90

Functions
int	jacobian_initialize_empty (Jacobian *jac, unsigned int num_spec)
	Initialize the Jacobian.

int	jacobian_initialize (Jacobian jac, unsigned int num_spec, unsigned int *jac_struct)
	Initialize the Jacobian.

int	jacobian_column_elements_add_space (JacobianColumnElements *column)

void	jacobian_register_element (Jacobian *jac, unsigned int dep_id, unsigned int ind_id)
	Adds an element to the sparse matrix.

int	compare_ids (const void a, const void b)

unsigned int	jacobian_build_matrix (Jacobian *jac)
	Builds the sparse matrix with the registered elements.

unsigned int	jacobian_number_of_elements (Jacobian jac)
	Returns the number of elements in the Jacobian.

unsigned int	jacobian_column_pointer_value (Jacobian jac, unsigned int col_id)
	Returns the value of a column pointer.

unsigned int	jacobian_row_index (Jacobian jac, unsigned int elem_id)
	Returns the row for a given Jacobian element.

unsigned int	jacobian_get_element_id (Jacobian jac, unsigned int dep_id, unsigned int ind_id)
	Get an element id in the Jacobian data arrays.

void	jacobian_reset (Jacobian jac)
	Reset the Jacobian.

void	jacobian_output (Jacobian jac, double *dest_array)
	Output the Jacobian.

void	jacobian_add_value (Jacobian jac, unsigned int elem_id, unsigned int prod_or_loss, long double jac_contribution)
	Add a contribution to the Jacobian.

void	jacobian_print (Jacobian jac)
	Prints the Jacobian structure.

void	jacobian_column_elements_free (JacobianColumnElements *column)
	Free memory associated with a JacobianColumnElements.

void	jacobian_free (Jacobian *jac)
	Free memory associated with a Jacobian.

Detailed Description

Jacobian functions.

Definition in file Jacobian.c.

Macro Definition Documentation

◆ BUFFER_SIZE

#define BUFFER_SIZE 10

Definition at line 17 of file Jacobian.c.

◆ SMALL_NUMBER

#define SMALL_NUMBER 1e-90

Definition at line 18 of file Jacobian.c.

Function Documentation

◆ compare_ids()

int compare_ids	(	const void *	a,
		const void *	b
	)

Definition at line 125 of file Jacobian.c.

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◆ jacobian_add_value()

void jacobian_add_value	(	Jacobian	jac,
		unsigned int	elem_id,
		unsigned int	prod_or_loss,
		long double	jac_contribution
	)

Add a contribution to the Jacobian.

Parameters

jac	Jacobian object
elem_id	Index of the element to update in the data array
prod_or_loss	Flag indicating whether to update the (0) production or (1) loss elements
jac_contribution	Value to add to the Jacobian element (contributions to loss elements should be positive if the contribution increases the loss)

Definition at line 234 of file Jacobian.c.

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◆ jacobian_build_matrix()

unsigned int jacobian_build_matrix ( Jacobian * jac )

Builds the sparse matrix with the registered elements.

Returns: 1 on success, 0 otherwise

Definition at line 129 of file Jacobian.c.

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◆ jacobian_column_elements_add_space()

int jacobian_column_elements_add_space ( JacobianColumnElements * column )

Definition at line 92 of file Jacobian.c.

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◆ jacobian_column_elements_free()

void jacobian_column_elements_free ( JacobianColumnElements * column )

Free memory associated with a JacobianColumnElements.

Parameters

column Jacobian column elements

Definition at line 274 of file Jacobian.c.

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◆ jacobian_column_pointer_value()

unsigned int jacobian_column_pointer_value	(	Jacobian	jac,
		unsigned int	col_id
	)

Returns the value of a column pointer.

Parameters

jac	Jacobian object
col_id	Column index (0...number of columns)

Returns: Column pointer value

Definition at line 192 of file Jacobian.c.

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◆ jacobian_free()

void jacobian_free ( Jacobian * jac )

Free memory associated with a Jacobian.

Parameters

jac	Jacobian object

Definition at line 281 of file Jacobian.c.

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◆ jacobian_get_element_id()

unsigned int jacobian_get_element_id	(	Jacobian	jac,
		unsigned int	dep_id,
		unsigned int	ind_id
	)

Get an element id in the Jacobian data arrays.

If the element is not included in the sparse matrix, -1 is returned.

Parameters

jac	Jacobian object
dep_id	Dependent species index
ind_id	Independent species index

Returns: Index of Jacobian element in the data array

Definition at line 200 of file Jacobian.c.

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◆ jacobian_initialize()

int jacobian_initialize	(	Jacobian *	jac,
		unsigned int	num_spec,
		unsigned int **	jac_struct
	)

Initialize the Jacobian.

Parameters

jac	Pointer to the Jacobian object
num_spec	Number of species
jac_struct	Dense matrix of flags indicating whether an element is (1) potentially non-zero or (0) not.

Returns: Flag indicating whether the derivative was successfully initialized (0 = false; 1 = true)

Definition at line 46 of file Jacobian.c.

◆ jacobian_initialize_empty()

int jacobian_initialize_empty	(	Jacobian *	jac,
		unsigned int	num_spec
	)

Initialize the Jacobian.

Sets up a sparse matrix (num_spec x num_spec) containing zero elements. Elements can be added using the jacobian_register_element function.

Parameters

jac	Jacobian object
num_spec	Number of species

Returns: Flag indicating whether the Jacobian was successfully initialized (0 = false; 1 = true)

Definition at line 20 of file Jacobian.c.

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◆ jacobian_number_of_elements()

unsigned int jacobian_number_of_elements ( Jacobian jac )

Returns the number of elements in the Jacobian.

Parameters

jac	Jacobian object

Returns: Number of Jacobian elements

Definition at line 190 of file Jacobian.c.

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◆ jacobian_output()

void jacobian_output	(	Jacobian	jac,
		double *	dest_array
	)

Output the Jacobian.

Parameters

jac	Jacobian object
dest_array	Pointer to the array to save Jacobian data to

Definition at line 223 of file Jacobian.c.

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◆ jacobian_print()

void jacobian_print ( Jacobian jac )

Prints the Jacobian structure.

Parameters

jac	Jacobian object

Definition at line 243 of file Jacobian.c.

◆ jacobian_register_element()

void jacobian_register_element	(	Jacobian *	jac,
		unsigned int	dep_id,
		unsigned int	ind_id
	)

Adds an element to the sparse matrix.

Parameters

jac	Jacobian object
dep_id	Dependent species index
ind_id	Independent species index

Definition at line 105 of file Jacobian.c.

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◆ jacobian_reset()

void jacobian_reset ( Jacobian jac )

Reset the Jacobian.

Parameters

jac	Jacobian matrix

Definition at line 216 of file Jacobian.c.

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◆ jacobian_row_index()

unsigned int jacobian_row_index	(	Jacobian	jac,
		unsigned int	elem_id
	)

Returns the row for a given Jacobian element.

Parameters

jac	Jacobian object
elem_id	Jacobian element index (0...number of elements-1)

Returns: Row index for given element

Definition at line 196 of file Jacobian.c.

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Macros

Functions

Detailed Description

Macro Definition Documentation

◆ BUFFER_SIZE

◆ SMALL_NUMBER

Function Documentation

◆ compare_ids()

◆ jacobian_add_value()

◆ jacobian_build_matrix()

◆ jacobian_column_elements_add_space()

◆ jacobian_column_elements_free()

◆ jacobian_column_pointer_value()

◆ jacobian_free()

◆ jacobian_get_element_id()

◆ jacobian_initialize()

◆ jacobian_initialize_empty()

◆ jacobian_number_of_elements()

◆ jacobian_output()

◆ jacobian_print()

◆ jacobian_register_element()

◆ jacobian_reset()

◆ jacobian_row_index()