/Users/huttone/Devel/sedflux-new/sedflux/trunk/ew/bio/bio_sed_interface.c File Reference

#include <glib.h>
#include <utils/utils.h>
#include <sed/sed_sedflux.h>
#include "bio.h"
#include <stdio.h>

Go to the source code of this file.

Classes

struct  Bio_param_t

Defines

#define BIO_PROCESS_NAME_S   "bioturbation"
#define EH_LOG_DOMAIN   BIO_PROCESS_NAME_S
#define BIO_KEY_DEPTH   "depth of bioturbation"
#define BIO_KEY_MODEL   "bioturbation model"
#define BIO_KEY_K   "diffusion coefficient"
#define BIO_KEY_R   "conveyor rate"

Functions

G_GNUC_INTERNAL Sed_cellbio_array_to_cell_array (Sed_cell *c_arr, double **data)
G_GNUC_INTERNAL double ** sed_array_to_bio_array (Sed_cell *c_arr, gint *n_grains, gint *n_layers)
G_GNUC_INTERNAL void sed_column_bioturbate (Sed_column c, double depth, double k, double duration, Bio_method m)
GOptionGroup * bio_get_option_group (void)
Sed_process_info bio_run (Sed_process proc, Sed_cube p)
gboolean bio_init (Sed_process p, Eh_symbol_table t, GError **error)
gboolean bio_destroy (Sed_process p)


Define Documentation

#define BIO_KEY_DEPTH   "depth of bioturbation"

Definition at line 113 of file bio_sed_interface.c.

Referenced by bio_init(), and init_bioturbation().

#define BIO_KEY_K   "diffusion coefficient"

Definition at line 115 of file bio_sed_interface.c.

Referenced by bio_init(), and init_bioturbation().

#define BIO_KEY_MODEL   "bioturbation model"

Definition at line 114 of file bio_sed_interface.c.

Referenced by bio_init().

#define BIO_KEY_R   "conveyor rate"

Definition at line 116 of file bio_sed_interface.c.

Referenced by bio_init().

#define BIO_PROCESS_NAME_S   "bioturbation"

Definition at line 1 of file bio_sed_interface.c.

#define EH_LOG_DOMAIN   BIO_PROCESS_NAME_S

Definition at line 2 of file bio_sed_interface.c.


Function Documentation

Sed_cell * bio_array_to_cell_array ( Sed_cell c_arr,
double **  data 
)

Definition at line 319 of file bio_sed_interface.c.

References eh_compare_dbl(), eh_exit(), eh_new0, eh_require_not_reached, eh_watch_dbl, eh_watch_int, sed_cell_add(), sed_cell_array_delete_empty(), sed_cell_array_mass(), sed_cell_fprint(), sed_cell_new_env(), and sed_cell_resize().

Referenced by sed_column_bioturbate().

gboolean bio_destroy ( Sed_process  p  ) 

Definition at line 188 of file bio_sed_interface.c.

References Bio_param_t::depth, eh_free, eh_input_val_destroy(), Bio_param_t::k, and sed_process_user_data().

GOptionGroup* bio_get_option_group ( void   ) 

Definition at line 38 of file bio_sed_interface.c.

Referenced by sedflux_parse_command_line().

gboolean bio_init ( Sed_process  p,
Eh_symbol_table  t,
GError **  error 
)

Definition at line 142 of file bio_sed_interface.c.

References BIO_ERROR, BIO_ERROR_BAD_ALGORITHM, BIO_KEY_DEPTH, BIO_KEY_K, BIO_KEY_MODEL, BIO_KEY_R, BIO_METHOD_CONVEYOR, BIO_METHOD_DIFFUSION, BIO_METHOD_UNKNOWN, Bio_param_t::depth, eh_require, eh_return_val_if_fail, eh_symbol_table_input_value(), eh_symbol_table_lookup(), eh_symbol_table_require_labels(), Bio_param_t::k, Bio_param_t::method, Bio_param_t::r, and sed_process_new_user_data.

Sed_process_info bio_run ( Sed_process  proc,
Sed_cube  p 
)

Definition at line 49 of file bio_sed_interface.c.

References BIO_METHOD_CONVEYOR, BIO_METHOD_DIFFUSION, Bio_param_t::depth, eh_input_val_eval(), eh_require, eh_require_not_reached, Bio_param_t::k, Bio_param_t::method, Bio_param_t::r, S_SECONDS_PER_DAY, S_SECONDS_PER_YEAR, sed_column_bioturbate(), sed_cube_age_in_years(), sed_cube_col(), sed_cube_size(), sed_cube_time_step_in_seconds(), SED_EMPTY_INFO, and sed_process_user_data().

double ** sed_array_to_bio_array ( Sed_cell c_arr,
gint *  n_grains,
gint *  n_layers 
)

Definition at line 295 of file bio_sed_interface.c.

References eh_require, sed_cell_nth_amount(), and sed_sediment_env_n_types().

void sed_column_bioturbate ( Sed_column  c,
double  depth,
double  k,
double  duration,
Bio_method  m 
)

Definition at line 205 of file bio_sed_interface.c.

References bio_array_to_cell_array(), bio_conveyor_layers(), bio_diffuse_layers(), BIO_METHOD_CONVEYOR, BIO_METHOD_DIFFUSION, eh_compare_dbl(), eh_dbl_array_sum(), eh_free, eh_new, eh_require, eh_require_not_reached, eh_watch_dbl, eh_watch_int, eh_watch_ptr, sed_cell_array_free(), sed_cell_size(), sed_column_extract_cells_above(), sed_column_mass(), sed_column_stack_cells_loc(), sed_column_top_height(), and sed_column_z_res().

Referenced by bio_run(), and run_bioturbation().


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