Photolysis reaction solver functions. More...

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Macros
#define	TEMPERATURE_K_ env_data[0]

#define	PRESSURE_PA_ env_data[1]

#define	NUM_REACT_ int_data[0]

#define	NUM_PROD_ int_data[1]

#define	RXN_ID_ int_data[2]

#define	SCALING_ float_data[0]

#define	RATE_CONSTANT_ (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

#define	REACT_(x) (int_data[NUM_INT_PROP_ + x] - 1)

#define	PROD_(x) (int_data[NUM_INT_PROP_ + NUM_REACT_ + x] - 1)

#define	DERIV_ID_(x) int_data[NUM_INT_PROP_ + NUM_REACT_ + NUM_PROD_ + x]

#define	JAC_ID_(x) int_data[NUM_INT_PROP_ + 2 * (NUM_REACT_ + NUM_PROD_) + x]

#define	YIELD_(x) float_data[NUM_FLOAT_PROP_ + x]

Functions
void	rxn_photolysis_get_used_jac_elem (int rxn_int_data, double rxn_float_data, Jacobian *jac)
	Flag Jacobian elements used by this reaction.

void	rxn_photolysis_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_photolysis_update_data (void update_data, int rxn_int_data, double rxn_float_data, double rxn_env_data)
	Update reaction data.

void	rxn_photolysis_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_photolysis_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_photolysis_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_photolysis_print (int rxn_int_data, double rxn_float_data)
	Print the Photolysis reaction parameters.

void *	rxn_photolysis_create_rate_update_data ()
	Create update data for new photolysis rates.

void	rxn_photolysis_set_rate_update_data (void *update_data, int photo_id, double base_rate)
	Set rate update data.

Detailed Description

Photolysis reaction solver functions.

Definition in file rxn_photolysis.c.

Macro Definition Documentation

◆ BASE_RATE_

#define BASE_RATE_ (rxn_env_data[1])

Definition at line 25 of file rxn_photolysis.c.

◆ DERIV_ID_

#define DERIV_ID_ ( x ) int_data[NUM_INT_PROP_ + NUM_REACT_ + NUM_PROD_ + x]

Definition at line 31 of file rxn_photolysis.c.

◆ JAC_ID_

#define JAC_ID_ ( x ) int_data[NUM_INT_PROP_ + 2 * (NUM_REACT_ + NUM_PROD_) + x]

Definition at line 32 of file rxn_photolysis.c.

◆ NUM_ENV_PARAM_

#define NUM_ENV_PARAM_ 2

Definition at line 28 of file rxn_photolysis.c.

◆ NUM_FLOAT_PROP_

#define NUM_FLOAT_PROP_ 1

Definition at line 27 of file rxn_photolysis.c.

◆ NUM_INT_PROP_

#define NUM_INT_PROP_ 3

Definition at line 26 of file rxn_photolysis.c.

◆ NUM_PROD_

#define NUM_PROD_ int_data[1]

Definition at line 21 of file rxn_photolysis.c.

◆ NUM_REACT_

#define NUM_REACT_ int_data[0]

Definition at line 20 of file rxn_photolysis.c.

◆ PRESSURE_PA_

#define PRESSURE_PA_ env_data[1]

Definition at line 18 of file rxn_photolysis.c.

◆ PROD_

#define PROD_ ( x ) (int_data[NUM_INT_PROP_ + NUM_REACT_ + x] - 1)

Definition at line 30 of file rxn_photolysis.c.

◆ RATE_CONSTANT_

#define RATE_CONSTANT_ (rxn_env_data[0])

Definition at line 24 of file rxn_photolysis.c.

◆ REACT_

#define REACT_ ( x ) (int_data[NUM_INT_PROP_ + x] - 1)

Definition at line 29 of file rxn_photolysis.c.

◆ RXN_ID_

#define RXN_ID_ int_data[2]

Definition at line 22 of file rxn_photolysis.c.

◆ SCALING_

#define SCALING_ float_data[0]

Definition at line 23 of file rxn_photolysis.c.

◆ TEMPERATURE_K_

#define TEMPERATURE_K_ env_data[0]

Definition at line 17 of file rxn_photolysis.c.

◆ YIELD_

#define YIELD_ ( x ) float_data[NUM_FLOAT_PROP_ + x]

Definition at line 33 of file rxn_photolysis.c.

Function Documentation

◆ rxn_photolysis_calc_deriv_contrib()

void rxn_photolysis_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 161 of file rxn_photolysis.c.

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◆ rxn_photolysis_calc_jac_contrib()

void rxn_photolysis_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 207 of file rxn_photolysis.c.

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◆ rxn_photolysis_create_rate_update_data()

void * rxn_photolysis_create_rate_update_data ( )

Create update data for new photolysis rates.

Returns: Pointer to a new rate update data object

Definition at line 262 of file rxn_photolysis.c.

◆ rxn_photolysis_get_used_jac_elem()

void rxn_photolysis_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 41 of file rxn_photolysis.c.

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◆ rxn_photolysis_print()

void rxn_photolysis_print	(	int *	rxn_int_data,
		double *	rxn_float_data
	)

Print the Photolysis 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 249 of file rxn_photolysis.c.

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◆ rxn_photolysis_set_rate_update_data()

void rxn_photolysis_set_rate_update_data	(	void *	update_data,
		int	photo_id,
		double	base_rate
	)

Set rate update data.

Parameters

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

Definition at line 277 of file rxn_photolysis.c.

◆ rxn_photolysis_update_data()

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

Update reaction data.

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

int photo_id (Id of one or more photolysis reactions set by the host model using the camp_rxn_photolysis::rxn_photolysis_t::set_photo_id function prior to initializing the solver.)
double rate_const (New pre-scaling rate constant.)

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 109 of file rxn_photolysis.c.

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◆ rxn_photolysis_update_env_state()

void rxn_photolysis_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 Photolysis reaction this only involves recalculating the rate constant.

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 137 of file rxn_photolysis.c.

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◆ rxn_photolysis_update_ids()

void rxn_photolysis_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 66 of file rxn_photolysis.c.

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Macros

Functions

Detailed Description

Macro Definition Documentation

◆ BASE_RATE_

◆ DERIV_ID_

◆ JAC_ID_

◆ NUM_ENV_PARAM_

◆ NUM_FLOAT_PROP_

◆ NUM_INT_PROP_

◆ NUM_PROD_

◆ NUM_REACT_

◆ PRESSURE_PA_

◆ PROD_

◆ RATE_CONSTANT_

◆ REACT_

◆ RXN_ID_

◆ SCALING_

◆ TEMPERATURE_K_

◆ YIELD_

Function Documentation

◆ rxn_photolysis_calc_deriv_contrib()

◆ rxn_photolysis_calc_jac_contrib()

◆ rxn_photolysis_create_rate_update_data()

◆ rxn_photolysis_get_used_jac_elem()

◆ rxn_photolysis_print()

◆ rxn_photolysis_set_rate_update_data()

◆ rxn_photolysis_update_data()

◆ rxn_photolysis_update_env_state()

◆ rxn_photolysis_update_ids()