Header file for program fit-layer. More...

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Macros
#define	MAXNUM_LINES 10000
	Maximum number of lines in input file.

#define	MAX_LINELENGTH 100
	Maximum length of any line in input file.

#define	MAXNUM_COMMENTLINES 1000
	Maximum number of comment lines of input file to copy to output file.

#define	MAX_COMMAND_LENGTH 1000
	Maximum number of characters of command to copy to output file.

#define	FALSE 0
	FALSE assigned to 0.

#define	TRUE 1
	TRUE assigned to 1.

#define	PI (4*atan(1.0))
	Sets constant PI to M_PI if that is defined; otherwise, computes PI as $4 \: tan^{-1}(1)$ .

#define	FARADAY 96485.3399
	Faraday constant in C/mol.

#define	SMALLNUM 2.2204460492503131e-16
	For comparing doubles with 0: Sets SMALLNUM to DBL_EPSILON or to GSL_DBL_EPSILON if they're defined; otherwise set to another small number.

#define	IS_ZERO(x) (fabs(x) < (SMALLNUM) ? (TRUE) : (FALSE))
	Evaluates to TRUE if \|x\| < SMALLNUM, FALSE otherwise.

#define	STREQ(s1, s2) (strcmp(s1,s2) == 0)
	Compares strings s1 and s2; evaluates to TRUE if strings are equal, FALSE if not.

#define	SQR(x) ((x) * (x))
	Computes the square of x.

#define	MAX(x, y) ((x) > (y) ? (x) : (y))
	Computes the maximum of x and y.

#define	MIN(x, y) ((x) < (y) ? (x) : (y))
	Computes the minimum of x and y.

#define	INDEX(i, j) ((i)*(nr+1)+(j))
	Computes the 1D index for concentration or alpha arrays, given pseudo-2D indices i (z index) and j (r index); uses column-major ordering.

Functions
void	convolve3 (int M, int N, double a, double scale1, double scale2, double invr, double *out)
	Calculates updates to the concentration in a layer by applying the Laplacian in cylindrical coordinates; also scales by $\theta D_{free}$ . More...

void	error (char *errorstring,...)
	Print an error message to stderr and exit with status EXIT_FAILURE. More...

void	print_usage_fit_layer (char *program)
	Print usage message and exit with status EXIT_FAILURE. More...

void	check_filename (char in, char out)
	Make sure that the filename is not too long. More...

double *	create_array (int N, char *string)
	Create an array of doubles of the specified size. More...

int	assemble_command (int argc, char argv[], char command)
	Create a string containing the command used to run the program. More...

void	calc_diffusion_curve_layer_fit_layer (int nt, int nz, int nr, int iprobe, int jprobe, int iz1, int iz2, int nolayer, double dt, double dr, double sd, double st, double alpha_so, double theta_so, double kappa_so, double alpha_sp, double theta_sp, double kappa_sp, double alpha_sr, double theta_sr, double kappa_sr, double dfree, double t, double s, double invr, double p)
	Calculates the concentration as a function of space and time and returns the probe concentration as a function of time. More...

Detailed Description

Header file for program fit-layer.

Author: David Lewis, CABI, NKI

Copyright: GNU Public License

Date: 2012-2013

Definition in file header.h.

Function Documentation

int assemble_command	(	int	argc,
		char *	argv[],
		char *	command
	)

Create a string containing the command used to run the program.

It can be very useful for the program's output file to have a comment line that contains the command used to run the program. This function assembles that command into a string from the argc and argv parameters so it can be added to the output file.

Parameters

[in]	argc	Argument count (parameter passed to main)
[in]	argv	Argument vector (parameter passed to main)
[out]	command	String containing the command line

Returns: Number of elements on the command line

Definition at line 91 of file io.c.

void calc_diffusion_curve_layer_fit_layer	(	int	nt,
		int	nz,
		int	nr,
		int	iprobe,
		int	jprobe,
		int	iz1,
		int	iz2,
		int	nolayer,
		double	dt,
		double	dr,
		double	sd,
		double	st,
		double	alpha_so,
		double	theta_so,
		double	kappa_so,
		double	alpha_sp,
		double	theta_sp,
		double	kappa_sp,
		double	alpha_sr,
		double	theta_sr,
		double	kappa_sr,
		double	dfree,
		double *	t,
		double *	s,
		double *	invr,
		double *	p
	)

Calculates the concentration as a function of space and time and returns the probe concentration as a function of time.

This function solves the diffusion equation in each layer $ k $ ,

$\frac{\partial c_k(\vec r, t)}{\partial t} = D_{free} \theta_k \nabla^2{c_k(\vec r, t)} + s/\alpha_k - \kappa_k c_k(\vec r, t) \quad ,$

subject to the continuity conditions at the interfaces between layers

$c(\vec r_k, t) = c(\vec r_{k+1}, t) \quad$

$\alpha_k \theta_k \nabla c(\vec r_k, t) = \alpha_{k+1} \theta_{k+1} \nabla c(\vec r_{k+1}, t) \quad$

and the boundary condition $c(\vec r, t) = 0$ (total absorption) at the top, the bottom, and the side of the cylinder, where

$c_k(\vec r, t)$ = concentration in layer $ k $

$D_{free}$ = free diffusion coefficient

$\theta_k$ = permeability in layer $ k $

$s_k(\vec r, t)$ = source in layer $ k $

$\alpha_k$ = extracellular volume fraction in layer $ k $

$\kappa_k$ = nonspecific clearance factor in layer $ k $

This function calls convolve3() to compute the Laplacian in cylindrical coordinates.

Parameters

[in]	nt	Number of support points in time
[in]	nz	Number of rows of concentration matrix
[in]	nr	Number of columns of concentration matrix
[in]	iprobe	z-index of probe location
[in]	jprobe	r-index of probe location
[in]	iz1	z-index of SR-SP boundary
[in]	iz2	z-index of SP-SO boundary
[in]	nolayer	Flag for whether to model a single homogeneous environment (true) or to model a 3-layer environment
[in]	dt	Spacing in time ( $t_{i+1} = t_i + \Delta t$ )
[in]	dr	Spacing in r (in this program, $\Delta z = \Delta r$ )
[in]	sd	Source delay (time before source starts)
[in]	st	Duration of source
[in]	alpha_so	Extracellular volume fraction in SO layer
[in]	theta_so	Permeability in SO layer
[in]	kappa_so	Nonspecific clearance factor in SO layer
[in]	alpha_sp	Extracellular volume fraction in SP layer
[in]	theta_sp	Permeability in SP layer
[in]	kappa_sp	Nonspecific clearance factor in SP layer
[in]	alpha_sr	Extracellular volume fraction in SR layer
[in]	theta_sr	Permeability in SR layer
[in]	kappa_sr	Nonspecific clearance factor in SR layer
[in]	dfree	Free diffusion coefficient
[in]	t	Time array
[in]	s	Source array
[in]	invr	Array for values
[out]	p	Probe array (concentration as a function of time)

Definition at line 94 of file model.c.

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void check_filename	(	char *	in,
		char *	out
	)

Make sure that the filename is not too long.

If the input string is not to big, copy it to the output string. Otherwise, exit with an error message. This function is used to check that the user input filename is not too long.

Parameters

[in]	in	Input string = the user input filename (or base filename)
[out]	out	Output string = the input string, if not too long

Definition at line 103 of file extras.c.

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void convolve3	(	int	M,
		int	N,
		double *	a,
		double	scale1,
		double	scale2,
		double *	invr,
		double *	out
	)

Calculates updates to the concentration in a layer by applying the Laplacian in cylindrical coordinates; also scales by $\theta D_{free}$ .

Calculates the update terms

$\mathbf{out} = s_1 \mathbf{L} * \mathbf{a} + \frac{s_2}{r} \mathbf{D} * \mathbf{a} \qquad (r \neq 0)$

or

$\mathbf{out} = s_1 \mathbf{L0} * \mathbf{a} \qquad (r = 0)$

where

$\mathbf{out}$ = output array

$ s_1, s_2 $ = scaling factors

$\mathbf{a}$ = input array (concentration)

$ * $ means convolution

$\mathbf{L}$ = 3x3 Laplace operator (see above)

$\mathbf{L0}$ = 3x3 Laplace operator modified for $ r = 0 $

$\mathbf{D}$ = 3x3 derivative operator for $ r $

Note that the index $ j = 1 $ corresponds to $ r = 0 $ .

Parameters

[in]	M	Number of columns of input matrix (z)
[in]	N	Number of rows of input matrix (r)
[in]	a	Input matrix (concentration, c)
[in]	scale1	Scaling factor #1
[in]	scale2	Scaling factor #2
[in]	invr	Vector of 1/r values
[out]	out	Output matrix