header.h

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// Constants

#define MAXNUM_LINES 10000

#define MAX_LINELENGTH 100

#define MAXNUM_COMMENTLINES 1000

#define MAX_COMMAND_LENGTH 1000

#define FALSE 0

#define TRUE 1

#ifdef M_PI
# define PI M_PI
#else
# define PI (4*atan(1.0))
#endif

#define FARADAY 96485.3399

#ifdef DBL_EPSILON
# define SMALLNUM DBL_EPSILON
#elif defined GSL_DBL_EPSILON
# define SMALLNUM GSL_DBL_EPSILON
#else
# define SMALLNUM 2.2204460492503131e-16
#endif


// Macros

#define IS_ZERO(x) (fabs(x) < (SMALLNUM) ? (TRUE) : (FALSE))

#define STREQ(s1,s2) (strcmp(s1,s2) == 0)

#define SQR(x) ((x) * (x))

#define MAX(x,y) ((x) > (y) ? (x) : (y))

#define MIN(x,y) ((x) < (y) ? (x) : (y))

/* Define a macro for calculating the 1D index of the arrays
 * from the 2D indices i and j, in order to make the code simpler.
 * The 2D indices are: i corresponds to z and j corresponds to r.
 * The number of rows in most of these matrices is (nr+1)
 */
#define INDEX(i,j) ((i)*(nr+1)+(j))


// Function prototypes

// convo.c
void convolve3(int M, int N, double *a, double scale1, double scale2, double *invr, double *out);

// extras.c
void error(char *errorstring, ...);

void print_usage_fit_layer(char *program);

void check_filename(char *in, char *out);

double *create_array(int N, char *string);

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

// model.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);