rxn_emission.c File Reference

Emission reaction solver functions. More...

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Macros
#define	TEMPERATURE_K_   env_data[0]
#define	PRESSURE_PA_   env_data[1]
#define	RXN_ID_   (int_data[0])
#define	SPECIES_   (int_data[1] - 1)
#define	DERIV_ID_   int_data[2]
#define	SCALING_   float_data[0]
#define	RATE_   (rxn_env_data[0])
#define	BASE_RATE_   (rxn_env_data[1])
#define	NUM_INT_PROP_   3
#define	NUM_FLOAT_PROP_   1
#define	NUM_ENV_PARAM_   2

Functions
void	rxn_emission_get_used_jac_elem (int *rxn_int_data, double *rxn_float_data, Jacobian *jac)
	Flag Jacobian elements used by this reaction.
void	rxn_emission_update_ids (ModelData *model_data, int *deriv_ids, Jacobian jac, int *rxn_int_data, double *rxn_float_data)
	Update the time derivative and Jacbobian array indices.
bool	rxn_emission_update_data (void *update_data, int *rxn_int_data, double *rxn_float_data, double *rxn_env_data)
	Update reaction data.
void	rxn_emission_update_env_state (ModelData *model_data, int *rxn_int_data, double *rxn_float_data, double *rxn_env_data)
	Update reaction data for new environmental conditions.
void	rxn_emission_calc_deriv_contrib (ModelData *model_data, TimeDerivative time_deriv, int *rxn_int_data, double *rxn_float_data, double *rxn_env_data, realtype time_step)
	Calculate contributions to the time derivative \(f(t,y)\) from this reaction.
void	rxn_emission_calc_jac_contrib (ModelData *model_data, Jacobian jac, int *rxn_int_data, double *rxn_float_data, double *rxn_env_data, realtype time_step)
	Calculate contributions to the Jacobian from this reaction.
void	rxn_emission_print (int *rxn_int_data, double *rxn_float_data)
	Print the reaction parameters.
void *	rxn_emission_create_rate_update_data ()
	Create update data for new emission rates.
void	rxn_emission_set_rate_update_data (void *update_data, int rxn_id, double base_rate)
	Set rate update data.

Detailed Description

Emission reaction solver functions.

Definition in file rxn_emission.c.

Macro Definition Documentation

BASE_RATE_

#define BASE_RATE_   (rxn_env_data[1])

Definition at line 25 of file rxn_emission.c.

DERIV_ID_

#define DERIV_ID_   int_data[2]

Definition at line 22 of file rxn_emission.c.

NUM_ENV_PARAM_

#define NUM_ENV_PARAM_   2

Definition at line 28 of file rxn_emission.c.

NUM_FLOAT_PROP_

#define NUM_FLOAT_PROP_   1

Definition at line 27 of file rxn_emission.c.

NUM_INT_PROP_

#define NUM_INT_PROP_   3

Definition at line 26 of file rxn_emission.c.

PRESSURE_PA_

#define PRESSURE_PA_   env_data[1]

Definition at line 18 of file rxn_emission.c.

RATE_

#define RATE_   (rxn_env_data[0])

Definition at line 24 of file rxn_emission.c.

RXN_ID_

#define RXN_ID_   (int_data[0])

Definition at line 20 of file rxn_emission.c.

SCALING_

#define SCALING_   float_data[0]

Definition at line 23 of file rxn_emission.c.

SPECIES_

#define SPECIES_   (int_data[1] - 1)

Definition at line 21 of file rxn_emission.c.

TEMPERATURE_K_

#define TEMPERATURE_K_   env_data[0]

Definition at line 17 of file rxn_emission.c.

Function Documentation

rxn_emission_calc_deriv_contrib()

void rxn_emission_calc_deriv_contrib	(	ModelData *	model_data,
		TimeDerivative	time_deriv,
		int *	rxn_int_data,
		double *	rxn_float_data,
		double *	rxn_env_data,
		realtype	time_step
	)

Calculate contributions to the time derivative \(f(t,y)\) from this reaction.

Parameters

model_data	Pointer to the model data, including the state array
time_deriv	TimeDerivative object
rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data
rxn_env_data	Pointer to the environment-dependent parameters
time_step	Current time step being computed (s)

Definition at line 133 of file rxn_emission.c.

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rxn_emission_calc_jac_contrib()

void rxn_emission_calc_jac_contrib	(	ModelData *	model_data,
		Jacobian	jac,
		int *	rxn_int_data,
		double *	rxn_float_data,
		double *	rxn_env_data,
		realtype	time_step
	)

Calculate contributions to the Jacobian from this reaction.

Parameters

model_data	Pointer to the model data
jac	Reaction Jacobian
rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data
rxn_env_data	Pointer to the environment-dependent parameters
time_step	Current time step being calculated (s)

Definition at line 160 of file rxn_emission.c.

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rxn_emission_create_rate_update_data()

void * rxn_emission_create_rate_update_data

(

)

Create update data for new emission rates.

Returns

Pointer to a new rate update data object

Definition at line 192 of file rxn_emission.c.

rxn_emission_get_used_jac_elem()

void rxn_emission_get_used_jac_elem	(	int *	rxn_int_data,
		double *	rxn_float_data,
		Jacobian *	jac
	)

Flag Jacobian elements used by this reaction.

Parameters

rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data
jac	Jacobian

Definition at line 36 of file rxn_emission.c.

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rxn_emission_print()

void rxn_emission_print	(	int *	rxn_int_data,
		double *	rxn_float_data
	)

Print the reaction parameters.

Parameters

rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data

Definition at line 179 of file rxn_emission.c.

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rxn_emission_set_rate_update_data()

void rxn_emission_set_rate_update_data	(	void *	update_data,
		int	rxn_id,
		double	base_rate
	)

Set rate update data.

Parameters

update_data	Pointer to an allocated rate update data object
rxn_id	Id of emission reactions to update
base_rate	New pre-scaling emission rate

Definition at line 207 of file rxn_emission.c.

rxn_emission_update_data()

bool rxn_emission_update_data	(	void *	update_data,
		int *	rxn_int_data,
		double *	rxn_float_data,
		double *	rxn_env_data
	)

Update reaction data.

Emission reactions can have their base (pre-scaling) rates updated from the host model based on the calculations of an external module. The structure of the update data is:

• int rxn_id (Id of one or more emission reactions set by the host model using the camp_rxn_emission::rxn_emission_t::set_rxn_id function prior to initializing the solver.)
• double rate (New pre-scaling rate.)

Parameters

update_data	Pointer to the updated reaction data
rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data
rxn_env_data	Pointer to the environment-dependent data

Returns

Flag indicating whether this is the reaction to update

Definition at line 82 of file rxn_emission.c.

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rxn_emission_update_env_state()

void rxn_emission_update_env_state	(	ModelData *	model_data,
		int *	rxn_int_data,
		double *	rxn_float_data,
		double *	rxn_env_data
	)

Update reaction data for new environmental conditions.

For emission reactions this only involves recalculating the rate.

Parameters

model_data	Pointer to the model data
rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data
rxn_env_data	Pointer to the environment-dependent parameters

Definition at line 109 of file rxn_emission.c.

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rxn_emission_update_ids()

void rxn_emission_update_ids	(	ModelData *	model_data,
		int *	deriv_ids,
		Jacobian	jac,
		int *	rxn_int_data,
		double *	rxn_float_data
	)

Update the time derivative and Jacbobian array indices.

Parameters

model_data	Pointer to the model data
deriv_ids	Id of each state variable in the derivative array
jac	Jacobian
rxn_int_data	Pointer to the reaction integer data
rxn_float_data	Pointer to the reaction floating-point data

Definition at line 52 of file rxn_emission.c.

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