Function prototypes for exported functions. More...

#include "rz_array.h"
#include "grid.h"
#include "interpol2.h"
#include "mapper.h"
#include "cdr.h"
#include "poisson.h"
#include "photo.h"
#include "reaction.h"

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Functions
rz_array_t *	rz_new_3d_a (int r0, int z0, int r1, int z1, int ntheta)
	Creates a new 3D array structure.

rz_array_t *	rz_guest (rz_array_t *host, int r0, int z0, int r1, int z1)
	Creates guest array: This is an array that contains part of another one.

void	rz_set_zero (rz_array_t *array)
	Sets the data of an array to zero.

void	rz_set_periodic (rz_array_t *array)
	Sets periodic boundary conditions for theta in an array.

void	rz_copy_bnd (rz_array_t from, rz_array_t to, int sign, REAL start_from, REAL start_to, int dim0, int inout_from, int inout_to, int dim1, int dim1_0, int dim1_1, int dim2, int dim2_0, int dim2_1)
	Sets boundaries for one array reading data from other array (but both can be the same: see rz_set_bnd).

void	rz_set_bnd (rz_array_t array, int sign, REAL start, int dim0, int inout, int dim1, int dim1_from, int dim1_to, int dim2, int dim2_from, int dim2_to)
	Sets boundary conditions (Neumann/Dirichlet) reading from the array itself.

void	rz_free (rz_array_t *array)
	Frees an array.

void	rz_copy (rz_array_t fro, int rfro, int zfro, rz_array_t to, int rto, int zto, int rn, int zn)
	Copies a sub-array of rn x zn from fro (starting at (rfro, zfro)) to to (starting at (rto, zto)).

void	rz_copy_modes (rz_array_t fro, int rfro, int zfro, rz_array_t to, int rto, int zto, int rn, int zn, int nmode_fro, int nmode_to)
	Copies a sub-array of the mode nmode of rn x zn from fro (starting at (rfro, zfro)) to to (starting at (rto, zto)).

void	rz_dump (rz_array_t rz_array, const char fname, const char *mode, int r0, int z0, int r1, int z1)
	Reads or writes a rz_array, depending on the string mode, "r" for reading, "w" for writing.

void	rz_dump_3d (rz_array_t rz_array, const char fname, const char *mode, int r0, int z0, int r1, int z1, int ntheta)
	rz_dump_3d QQQQ

void	rz_axis_dump (const char *fname, int x0, int x1, double delta)
	rz_axis_dump QQQQ

int	grid_max_depth_r (grid_t *grid)
	Gets the maximum depth of a tree (the level of its deepest node)

double	grid_rmin_r (grid_t *grid)
	Gets the minimum r of a grid and all its descendants.

void	grid_print_r (grid_t *grid, int indent)
	Recursively prints one grid and all its descendants.

int	grid_contains (grid_t *grid, int i, int j, int check)
	Checks whether a point is in the interior or on a given boundary of a grid.

int	grid_overlap (grid_t grid1, grid_t grid2, int buff1, int buff2, int left, int bottom, int right, int top, int *level_diff)
	Checks whether two grids overlap and return the rectangle that they in common.

int	grid_overlap_with_shifts (grid_t grid1, grid_t grid2, int buff1, int buff2, int left, int bottom, int right, int top, int *level_diff, int shift_r, int shift_z)
	Checks the overlap between two grids.

void	grid_inherit_ext_bound (grid_t *grid)
	Makes a grid inherit the ext_bound field of its parent,.

grid_t *	grid_finest_containing_r (grid_t *grid, double r, double z)
	Finds the finest descendant of grid that contains the point given by the (r, z) coordinates.

int	grid_howmany_children (grid_t *grid)
	How many children does one grid have?

grid_t *	grid_get_child (grid_t *grid, int n)
	Finds child number n of the given grid.

interpol_t *	interpol_new_a (double Lr, double Lz, interpol_method_t *method)
	Creates a new interpolator that uses a given method.

void	interpol_free (interpol_t *this)
	Frees the interpolator.

void	interpol_set_stencil (interpol_t *this, double r0, double z0,...)
	Sets the stencil of the interpolation object.

void	interpol_set_stencil_at (grid_t grid, interpol_t this, double r0, double z0, rz_array_t *ar, int ir, int iz, int itheta)
	Sets the stencil reading from an array.

void	interpol_set_coeffs (interpol_t *this)
	Calculates the coefficients of the interpolating polynomial.

double	interpol_apply (interpol_t *this, double r, double z)
	Evaluates the interpolating polynomial.

void	map_grid (mapper_t *mappers, grid_t source, grid_t *target, int ntheta, int copy, int interpol, int coarsen, int s_buff, int t_buff)
	Maps two grids.

void	map_grid_r (mapper_t *mappers, grid_t source, grid_t *target, int ntheta, int copy, int interpol, int coarsen, int s_buff, int t_buff)
	Recursive version of map_grid.

void	map_trees_r (mapper_t *mappers, grid_t source, grid_t *target, int ntheta, int copy, int interpol, int coarsen, int s_buff, int t_buff)
	Double-recursive version:

void	cdr_init (void)
	Some initialization is needed for this module which has to be inside this function.

void	cdr_end (void)
	And the cleaning up has to be here.

cdr_grid_t *	cdr_new_3d_a (int r0, int z0, int r1, int z1, int ntheta)
	Creates a new 3D cdr grid.

cdr_grid_t *	cdr_like_a (cdr_grid_t *grid)
	Returns a grid with the same dimensions as grid and at the same level.

cdr_grid_t *	cdr_clone_a (cdr_grid_t *grid)
	Returns a grid exactly like te one received, with the densities copied.

void	cdr_set_periodic (cdr_grid_t *grid)
	Impose periodic boundary conditions in $\theta$ on a grid.

void	cdr_free (cdr_grid_t *grid)

void	cdr_free_r (cdr_grid_t *grid)
	Recursive version of cdr_free.

void	cdr_calc_charge (cdr_grid_t *grid)
	Calculates the charge in a CDR grid.

void	cdr_calc_charge_r (cdr_grid_t *root)

void	cdr_dft_charge_r (cdr_grid_t *grid, int sign)

cdr_grid_t *	cdr_create_coarser_a (cdr_grid_t *grid)
	Creates a grid one level coarser than GRID that covers the same area or somewhat more.

cdr_grid_t *	cdr_add_coarser_grids_a (cdr_grid_t *prev_root, int n)
	Takes a tree of input nodes and adds n coarser grids, returning a pointer to the root leaf.

void	cdr_free_coarser_grids (cdr_grid_t *prev_root, int n)
	Frees the memory allocated by cdr_add_coarser_grids_a.

void	cdr_add_ext_field (cdr_grid_t *grid)
	Adds an external electric field to a cdr grid.

void	cdr_add_ext_field_r (cdr_grid_t *grid)

void	cdr_add_inhom_field_r (cdr_grid_t *cdr, double q)

void	cdr_calc_eabs (cdr_grid_t *grid)
	Calculates the absolute value of the electric field by linear interpolation of its components.

void	cdr_calc_eabs_r (cdr_grid_t *grid)

void	cdr_nonegative (cdr_grid_t *grid)

void	cdr_nonegative_r (cdr_grid_t *grid)

pois_grid_t **	cdr_calc_field_r (cdr_grid_t *grid, int return_pois)
	The interface between the cdr and the poisson parts.

void	cdr_set_ext_bnd (cdr_grid_t *grid)

void	cdr_set_ext_bnd_r (cdr_grid_t *grid)

void	cdr_calc_d_dens (cdr_grid_t *grid)
	Calculates the derivatives of the densities for each point of the grid.

void	cdr_calc_d_dens_r (cdr_grid_t *grid)

void	cdr_advect_diffu (cdr_grid_t *grid)
	Adds the advection and diffusion terms to the derivatives of the densities.

void	cdr_advect_diffu_r (cdr_grid_t *grid)

double	cdr_courant (cdr_grid_t *grid)
	Returns the minimum tau that satisfies the Courant-Friedrichs-Lewy restriction (CFL).

void	cdr_update (cdr_grid_t orig, cdr_grid_t dest, double h)
	Writes into the densities of the grid dest the densities of grid orig plus its derivatives times h.

void	cdr_rk2_update (cdr_grid_t dens_0, cdr_grid_t d_dens_1, cdr_grid_t d_dens_2, cdr_grid_t dest, double h)
	Sets dest->dens = dens_0->dens + h/2 * d_dens_1->d_dens + h/2 * d_dens_2->d_dens.

void	cdr_rk2_update_r (cdr_grid_t dens_0, cdr_grid_t d_dens_1, cdr_grid_t d_dens_2, cdr_grid_t dest, double h)
	Recursive version of cdr_rk2_update.

void	cdr_self_update_r (cdr_grid_t *grid, double h)
	Recursive version of the former QQQQ, used to implement Euler integration.

void	cdr_like_update_ar (cdr_grid_t grid, cdr_grid_t new_grid, double h)
	Yet another recursive version of cdr_update, used to implement higher order Runge-Kutta integrations.

double	cdr_rk2 (cdr_grid_t *grid, double h, double t)
	Computes the grid error. QQQQ.

void	cdr_update_refined (cdr_grid_t **ptree)
	Takes a pointer to a family of cdr grids, creates a new family which is stored in that pointer and takes rid of the initial family.

void	cdr_calc_maxs (cdr_grid_t *grid)
	Updates the values of max_dens and max_charge.

void	cdr_refine (cdr_grid_t *grid)
	Uses the previous routines to refine (if needed) a cdr grid.

void	cdr_refine_r (cdr_grid_t grid, cdr_grid_t source)
	Recursively refines a cdr grid and constructs a tree based on it.

void	cdr_match_r (cdr_grid_t grid1, cdr_grid_t grid2)
	Examines pairs of grids and matches them and all their descendants.

void	cdr_set_bnd (cdr_grid_t *grid)
	Sets the boundary conditions of all children of grid by interpolating from grid itself.

void	cdr_set_bnd_r (cdr_grid_t *grid)

void	cdr_restrict (cdr_grid_t *grid)
	Restricts a grid with all its children.

void	cdr_restrict_r (cdr_grid_t *grid)

void	cdr_set_dens (cdr_grid_t cdr, int species, int mode, double factor, double(f)(double, double, double))
	Sets the densities of species species according to the function .

void	cdr_init_dens (cdr_grid_t *cdr)
	Inits the densities of all species.

cdr_grid_t *	cdr_scratch_init (void)
	Initializes the densities allocating a new grid family.

mapper_t **	cdr_mappers_a (interpol_method_t *interp_method)

void	cdr_free_mappers (mapper_t **mappers)
	Frees the memory of all mappers QQQQ.

void	cdr_dump (cdr_grid_t grid, const char prefix, const char *name)
	Dumps all the contents of the given grid into filenames given by prefix and name.

void	cdr_dump_r (cdr_grid_t grid, const char prefix, const char name, FILE infp, double sim_time)
	Dumps all the contents of the given grid into filenames given by prefix and name.

cdr_grid_t *	cdr_load_tree_r (const char prefix, const char name, FILE *infp)
	Reads the data format produced by cdr_dump_r and creates a complete tree from it.

void	cdr_dump_frames (cdr_grid_t grid, const char prefix, const char *name)
	Given a grid family, writes in the file named fname the coordinates of the frames that define the grid and his descendants.

void	pois_init (void)
	All initialization of the Poisson solver has to be here.

pois_grid_t *	pois_new_a (int r0, int z0, int r1, int z1)
	Creates a 2D Poisson grid.

pois_grid_t *	pois_new_3d_a (int r0, int z0, int r1, int z1, int ntheta)
	Creates a new 3D Poisson grid.

void	pois_free (pois_grid_t *grid)
	Frees the memory allocated by pois_new_a.

void	pois_free_r (pois_grid_t *grid)
	Recursively frees a tree of Poisson grids.

pois_grid_t *	pois_new_glob_a (int r0, int z0, int r1, int z1, int level)
	Creates a new Poisson grid.

pois_grid_t *	pois_init_tree_a (int r0, int z0, int r1, int z1)
	Starts the tree of Poisson grids with the two coarsest ones.

REAL *	pois_boundary_a (pois_grid_t *grid, int boundary)
	Is it possible to use a single function to handle all four boundaries?

void	pois_solve_grid (pois_grid_t grid, pois_problem_t prob, double lambda, double s)
	Solves the Poisson equation, calling the FISHPACK routine.

void	pois_set_phi_boundaries (pois_grid_t grid, REAL boundaries[], int left_uns, int right_neu, int bottom_neu, int top_neu)
	Uses the boundaries[] vectors to set the boundaries by interpolation for the phi array of a grid.

int	pois_map_charge (pois_grid_t pois, cdr_grid_t cdr, int mode)

void	pois_set_error (pois_grid_t *grid)
	Estimates the error on this grid by comparing with the calculations for his parent and performing a Richardson extrapolation.

int	pois_refine (pois_grid_t *grid, double threshold)
	The refinement routine.

pois_grid_t **	pois_solve_a (cdr_grid_t cdr, pois_problem_t prob)
	Takes a cdr tree and solves the Poisson equation for it.

pois_grid_t **	pois_gen_solve_a (cdr_grid_t cdr, pois_problem_t prob, mapper_t **mappers, double es)
	Solves a Poisson/Helmholtz equation with FISHPACK and maps the result using a given set of mapper.

pois_grid_t *	pois_solve_mode (cdr_grid_t tree, cdr_grid_t cdr, pois_problem_t *prob, int mode, double es)
	Solves a single Fourier mode.

void	pois_solve_r (pois_grid_t pois, cdr_grid_t cdr, pois_problem_t *prob, int mode, double es, double threshold)
	Recursively solves one Poisson grid.

double	pois_phi_at (pois_grid_t *grid, double r, double z, double theta)
	Finds the best-possible approximation for the potential at a given point (r, z, theta) by interpolating from the finest grid that covers that point.

void	pois_dump (pois_grid_t grid, const char prefix, const char *name)
	Dumps all the contents of the given grid into filenames given by prefix and name.

void	pois_dump_r (pois_grid_t grid, const char prefix, const char *name)
	Dumps all the contents of the given grid into filenames given by prefix and name.

void	pois_write_error_r (pois_grid_t grid, FILE fp)
	Writes some error measures of this grid and its descendants into fp.

void	pois_error_measures (pois_grid_t grid, double L1, double L2, double Lmax)
	Calculates the error measure of this grid.

void	pois_inhom_init (void)
	pois_inhom_init QQQQ

double	pois_inhom_phi (double r, double z)
	Returns the potential created by a unit charge located at pois_inhom_z between an electrode at 0 and a second one at pois_inhom_L.

double	pois_inhom_er (double r, double z)
	Radial component of the field.

double	pois_inhom_ez (double r, double z)
	Axial component of the field.

double	pois_inhom_q_factor (pois_grid_t *pois)
	Once we have the electrostatic potential created by the space charges, we use this function to compute the multiplying factor of the floating charge.

void	pois_add_inhom_phi_r (pois_grid_t *grid, double q)
	Adds the potential created by the needle to a Poisson grid and their descendants.

void	photo_init ()
	Initializes photoionization QQQQ?

void	photo_register (double A, double lambda)
	Registers a photoionization term with given A and lambda.

void	photo_copy_list (photo_term_t src, photo_term_t *dest)
	Copies a list of photo terms into *dest.

void	photo_unregister_all (void)
	Unregisters all the photoionization terms and frees the allocated space.

void	photo_dft_r (cdr_grid_t *grid, int sign)
	Transforms back the photoionization calculation into real space.

void	photo_copy_source (cdr_grid_t *grid)
	Copies the derivative of the ion density into cdr->charge.

void	photo_add_term (photo_term_t term, cdr_grid_t cdr)

void	photo_add_term_r (photo_term_t term, cdr_grid_t cdr)
	...and the recursive version of photo_add_term

pois_grid_t **	photo_calc_term (photo_term_t term, cdr_grid_t cdr, int i)
	photo_calc_term QQQQ

void	photo_calc (photo_term_t terms, cdr_grid_t cdr)
	Calculates the photoionization and adds it to the derivatives of the species densities.

void	photo_load_file (char *fname)
	Loads a photoionization file, consisting in a series of rows with A and lambda.

void	init_parameters (void)
	Initializes the parameters.

void	cstream_init (void)
	Here all the initialization calls.

void	cstream_end (void)
	Here all the cleaning and finishing calls.

void	cstream_set_field_at_time (double t)
	When we use a time-varying external field, we update the field components at each timesteps.

void	dft_transform (rz_array_t in, rz_array_t out, int sign)
	Transform the discrete fourier transformations ????

void	dft_diff (grid_t grid, rz_array_t f)
	Calculates the Fourier transform of the derivative of a function given its Fourier transform.

void	dft_weight (cdr_grid_t cdr, rz_array_t var, double weights[], double power)
	Calculates the weight for a given cdr grid and a variable ???

void	dft_out_weights (cdr_grid_t grid, const char prefix, double t)
	Outputs to a file 'weights.tsv' the results of dft_weight.

void	dft_perturb (cdr_grid_t cdr, rz_array_t var, double *epsilon_k)
	Perturbs a FFT-transformed variable.

void	dft_dens_perturb_r (cdr_grid_t grid, int species, double epsilon_k)
	Takes a density in real space, transforms it to Fourier space, perturbs it and then transforms back to real space.

int	find_species_by_name (const char *spec_name)
	Returns the position in the species-array of a given species.

void	react_add (reaction_t *react)
	Adds a given reaction to the reaction list.

void	react_init ()
	Initializes the list of reactions.

void	react_apply_r (reaction_t react, cdr_grid_t grid, int overwrite)
	Recursive version of react_apply.

void	react_apply_all (cdr_grid_t *grid)
	Applies all reactions to the given grid and his descendants.

void	kinetic_init (void)
	Any initialization required by the kinetic model, has to be done in this function.

double	spr_density_at (double altitude)
	The density at a given height, assuming dens = 1.0 at height = 0.0.

void	spr_init ()
	Initialize the sprite module.

void	spr_hook (cdr_grid_t *grid)
	Hook to update the variables that depend on the head altitude.

void	spr_update (double altitude)
	Updates the magnitudes that we are tracking according to a given altitude.

double	spr_head_altitude (cdr_grid_t *grid, int sign)
	Finds the position of the streamer head by locating the maximum (or -maximum) of the charge along the streamer axis.

void	read_input_file (const char f_kinetic_name, const char filename)
	Reads the kinetic parameters (species, reactions) from file filename.

Detailed Description

Function prototypes for exported functions.

Definition in file proto.h.

Function Documentation

rz_array_t* rz_new_3d_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1,
		int	ntheta
	)

Creates a new 3D array structure.

Definition at line 23 of file rz_array.c.

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rz_array_t* rz_guest	(	rz_array_t *	host,
		int	r0,
		int	z0,
		int	r1,
		int	z1
	)

Creates guest array: This is an array that contains part of another one.

We use the memory of the original array and do not allocate new memory.

Definition at line 105 of file rz_array.c.

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void rz_set_zero ( rz_array_t * array )

Sets the data of an array to zero.

Definition at line 145 of file rz_array.c.

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void rz_set_periodic ( rz_array_t * array )

Sets periodic boundary conditions for theta in an array.

Definition at line 153 of file rz_array.c.

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void rz_copy_bnd	(	rz_array_t *	from,
		rz_array_t *	to,
		int	sign,
		REAL *	start_from,
		REAL *	start_to,
		int	dim0,
		int	inout_from,
		int	inout_to,
		int	dim1,
		int	dim1_0,
		int	dim1_1,
		int	dim2,
		int	dim2_0,
		int	dim2_1
	)

Sets boundaries for one array reading data from other array (but both can be the same: see rz_set_bnd).

Starting at *start_xxx, it sweeps a 2-dimensional subspace of the grid in dimensions dim1 and dim2 (and perpendicular to dim0). There it sets the boudary conditions.

The value of from is multiplied by sign. Thus, if the boundary is itself, is -1 for homogeneous dirichlet and 1 for homogeneous Neumann (though you should better use BND_CND_HNEUMANN and BND_CND_HDIRICHLET)

inout is -1 if we look/set the values on smaller values of dim0 1 if we look at larger values. (though it is better to use BND_INWARD=-1 and BND_OUTWARD=1).

Note: it is better to call this function before rz_set_periodic.

Definition at line 196 of file rz_array.c.

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void rz_set_bnd	(	rz_array_t *	array,
		int	sign,
		REAL *	astart,
		int	dim0,
		int	inout,
		int	dim1,
		int	dim1_0,
		int	dim1_1,
		int	dim2,
		int	dim2_0,
		int	dim2_1
	)

Sets boundary conditions (Neumann/Dirichlet) reading from the array itself.

For example, to set Neumann conditions at r = 0 (dim0 = R_INDX), we call it as

rz_set_bnd (array, 1, RZTP (array, 0, 0, 0), R_INDX, 1, Z_INDX, z0, z1, THETA_INDX, 0, ntheta);

Definition at line 229 of file rz_array.c.

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void rz_free ( rz_array_t * array )

Frees an array.

Definition at line 240 of file rz_array.c.

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void rz_copy	(	rz_array_t *	fro,
		int	rfro,
		int	zfro,
		rz_array_t *	to,
		int	rto,
		int	zto,
		int	rn,
		int	zn
	)

Copies a sub-array of rn x zn from fro (starting at (rfro, zfro)) to to (starting at (rto, zto)).

Definition at line 252 of file rz_array.c.

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void rz_copy_modes	(	rz_array_t *	fro,
		int	rfro,
		int	zfro,
		rz_array_t *	to,
		int	rto,
		int	zto,
		int	rn,
		int	zn,
		int	nmode_fro,
		int	nmode_to
	)

Copies a sub-array of the mode nmode of rn x zn from fro (starting at (rfro, zfro)) to to (starting at (rto, zto)).

Definition at line 277 of file rz_array.c.

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void rz_dump	(	rz_array_t *	rz_array,
		const char *	fname,
		const char *	mode,
		int	r0,
		int	z0,
		int	r1,
		int	z1
	)

Reads or writes a rz_array, depending on the string mode, "r" for reading, "w" for writing.

Note however that we must already have the dimensions of the array in it.

Definition at line 305 of file rz_array.c.

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void rz_dump_3d	(	rz_array_t *	rz_array,
		const char *	fname,
		const char *	mode,
		int	r0,
		int	z0,
		int	r1,
		int	z1,
		int	ntheta
	)

rz_dump_3d QQQQ

Definition at line 354 of file rz_array.c.

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void rz_axis_dump	(	const char *	fname,
		int	x0,
		int	x1,
		double	delta
	)

rz_axis_dump QQQQ

Definition at line 411 of file rz_array.c.

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int grid_max_depth_r ( grid_t * grid )

Gets the maximum depth of a tree (the level of its deepest node)

Definition at line 15 of file grid.c.

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double grid_rmin_r ( grid_t * grid )

Gets the minimum r of a grid and all its descendants.

Definition at line 30 of file grid.c.

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void grid_print_r	(	grid_t *	grid,
		int	indent
	)

Recursively prints one grid and all its descendants.

Definition at line 48 of file grid.c.

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int grid_contains	(	grid_t *	grid,
		int	i,
		int	j,
		int	check
	)

Checks whether a point is in the interior or on a given boundary of a grid.

Does the grid contain the point (i, j) (in its own coordinates)?
check has the following meaning:
GRID_INSIDE : Checks if the point is in the interior of the grid
BND_MASK_* : Checks if it is on the given boundary (BND_MASK_ALL checks for any boundary).

Definition at line 73 of file grid.c.

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int grid_overlap	(	grid_t *	grid1,
		grid_t *	grid2,
		int	buff1,
		int	buff2,
		int *	left,
		int *	bottom,
		int *	right,
		int *	top,
		int *	level_diff
	)

Checks whether two grids overlap and return the rectangle that they in common.

Checks whether two grids overlap and return the rectangle that they have in common in the coordinates of the finest grid in (*left, *bottom) - (*right, *top)

Note that *left, *bottom... can be modified even if the two grids do not overlap. buff1 and buff2 are integers that specify the numbers of cells that are taken as buffer in the boundaries for grid1 and grid2.

Definition at line 124 of file grid.c.

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int grid_overlap_with_shifts	(	grid_t *	grid1,
		grid_t *	grid2,
		int	buff1,
		int	buff2,
		int *	left,
		int *	bottom,
		int *	right,
		int *	top,
		int *	level_diff,
		int	shift_r,
		int	shift_z
	)

Checks the overlap between two grids.

Checks the overlap between two grids before it shifts the coarser grid by (shift_r << (level_diff - 1), shift_z << (level_diff - 1) (in finer grid coordinates).

Q: WTF! WHY!!!?
A: We use this to implement the mapping between electric fields. Since The electric field is evaluated not in the cell centers but in the borders, when we interpolate we have to take a shift into account. See mapper.c and mapper.h for more info.

Definition at line 145 of file grid.c.

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void grid_inherit_ext_bound ( grid_t * grid )

Makes a grid inherit the ext_bound field of its parent,.

with the appropiate modifications.

Definition at line 205 of file grid.c.

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grid_t* grid_finest_containing_r	(	grid_t *	grid,
		double	r,
		double	z
	)

Finds the finest descendant of grid that contains the point given by the (r, z) coordinates.

Or NULL if the point is not contained in grid. We assume that only ONE sub-grid can contain a given point.

Definition at line 245 of file grid.c.

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int grid_howmany_children ( grid_t * grid )

How many children does one grid have?

Definition at line 267 of file grid.c.

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grid_t* grid_get_child	(	grid_t *	grid,
		int	n
	)

Finds child number n of the given grid.

If it doesn't have enough children just returns NULL

Definition at line 284 of file grid.c.

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interpol_t* interpol_new_a	(	double	Lr,
		double	Lz,
		interpol_method_t *	method
	)

Creates a new interpolator that uses a given method.

Definition at line 49 of file interpol2.c.

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void interpol_free ( interpol_t * this )

Frees the interpolator.

Definition at line 70 of file interpol2.c.

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void interpol_set_stencil	(	interpol_t *	this,
		double	r0,
		double	z0,
			...
	)

Sets the stencil of the interpolation object.

r0 and z0 are the coordinates of the bottom-left corner of the stencil (the [0,0] point).

Definition at line 83 of file interpol2.c.

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void interpol_set_stencil_at	(	grid_t *	grid,
		interpol_t *	this,
		double	r0,
		double	z0,
		rz_array_t *	ar,
		int	ir,
		int	iz,
		int	itheta
	)

Sets the stencil reading from an array.

ir, iz give the index of the cell in the array corresponding to the stencil origin.

Definition at line 116 of file interpol2.c.

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void interpol_set_coeffs ( interpol_t * this )

Calculates the coefficients of the interpolating polynomial.

Has to be called after interpol_set_stencil.

Definition at line 161 of file interpol2.c.

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double interpol_apply	(	interpol_t *	this,
		double	r,
		double	z
	)

Evaluates the interpolating polynomial.

Definition at line 190 of file interpol2.c.

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void map_grid	(	mapper_t **	mappers,
		grid_t *	source,
		grid_t *	target,
		int	ntheta,
		int	copy,
		int	interpol,
		int	coarsen,
		int	s_buff,
		int	t_buff
	)

Maps two grids.

The arguments copy, interpol and coarsen are booleans that specify whether we should apply these methods in the mapping.

Definition at line 41 of file mapper.c.

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void map_grid_r	(	mapper_t **	mappers,
		grid_t *	source,
		grid_t *	target,
		int	ntheta,
		int	copy,
		int	interpol,
		int	coarsen,
		int	s_buff,
		int	t_buff
	)

Recursive version of map_grid.

Recurses over the source tree depth-first

Definition at line 105 of file mapper.c.

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void map_trees_r	(	mapper_t **	mappers,
		grid_t *	source,
		grid_t *	target,
		int	ntheta,
		int	copy,
		int	interpol,
		int	coarsen,
		int	s_buff,
		int	t_buff
	)

Double-recursive version:

Also recurses over the target tree.

Definition at line 126 of file mapper.c.

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void cdr_init ( void )

Some initialization is needed for this module which has to be inside this function.

Definition at line 80 of file cdr.c.

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void cdr_end ( void )

And the cleaning up has to be here.

Definition at line 95 of file cdr.c.

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cdr_grid_t* cdr_new_3d_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1,
		int	ntheta
	)

Creates a new 3D cdr grid.

Definition at line 103 of file cdr.c.

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cdr_grid_t* cdr_like_a ( cdr_grid_t * grid )

Returns a grid with the same dimensions as grid and at the same level.

Realize that the data is not copied into the new grid.

Definition at line 234 of file cdr.c.

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cdr_grid_t* cdr_clone_a ( cdr_grid_t * grid )

Returns a grid exactly like te one received, with the densities copied.

But the descendants are ignored.

Definition at line 255 of file cdr.c.

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void cdr_set_periodic ( cdr_grid_t * grid )

Impose periodic boundary conditions in $\theta$ on a grid.

Definition at line 288 of file cdr.c.

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void cdr_free ( cdr_grid_t * grid )

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void cdr_free_r ( cdr_grid_t * grid )

Recursive version of cdr_free.

Definition at line 341 of file cdr.c.

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void cdr_calc_charge ( cdr_grid_t * grid )

Calculates the charge in a CDR grid.

Important Note: The charge is here divided by ntheta because our FFT functions are unnormalized and hence when they are applied forth and back they return the initial value multiplied by ntheta. I believe that this is the best point to normalize the data.

Definition at line 361 of file cdr.c.

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void cdr_calc_charge_r ( cdr_grid_t * root )

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void cdr_dft_charge_r	(	cdr_grid_t *	grid,
		int	sign
	)

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cdr_grid_t* cdr_create_coarser_a ( cdr_grid_t * grid )

Creates a grid one level coarser than GRID that covers the same area or somewhat more.

Note: The new grid contains information only about the charge, not the other functions. That's why we don't use cdr_restrict.

Note that here we may be going one cell out of the aparent boundaries of the input grids but we allocated enough memory for that.

Definition at line 435 of file cdr.c.

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cdr_grid_t* cdr_add_coarser_grids_a	(	cdr_grid_t *	prev_root,
		int	n
	)

Takes a tree of input nodes and adds n coarser grids, returning a pointer to the root leaf.

Definition at line 480 of file cdr.c.

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void cdr_free_coarser_grids	(	cdr_grid_t *	prev_root,
		int	n
	)

Frees the memory allocated by cdr_add_coarser_grids_a.

Note: be careful to pass here only a tree returned by cdr_add_coarser_grids_a, since some grids may lose their references and stay allocated forever otherwise. (see assert below).

Definition at line 508 of file cdr.c.

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void cdr_add_ext_field ( cdr_grid_t * grid )

Adds an external electric field to a cdr grid.

Really, it would be more efficient to include that field in some other routine and we will avoid one more grid sweep. However, for the sake of code clarity, extendability and maintenability I prefer to add it here.

ext_e_r, ext_e_z and ext_e_theta are functions of three real numbers (r, z, $\theta$ ) that return each of the components of the electric field.

Note that it is the responsibility of e_theta to behave correctly (i.e. periodically) when it receives thetas outside $[0, 2 \pi]$ .

Definition at line 595 of file cdr.c.

void cdr_add_ext_field_r ( cdr_grid_t * grid )

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void cdr_add_inhom_field_r	(	cdr_grid_t *	cdr,
		double	q
	)

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void cdr_calc_eabs ( cdr_grid_t * grid )

Calculates the absolute value of the electric field by linear interpolation of its components.

Of course, it requires that all the components are already present.

Definition at line 668 of file cdr.c.

void cdr_calc_eabs_r ( cdr_grid_t * grid )

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void cdr_nonegative ( cdr_grid_t * grid )

void cdr_nonegative_r ( cdr_grid_t * grid )

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pois_grid_t** cdr_calc_field_r	(	cdr_grid_t *	cdr,
		int	return_pois
	)

The interface between the cdr and the poisson parts.

If return_pois is true, returns the Poisson trees and they have to be de-allocated by the calling program. If not, takes care himself of deallocation and returns NULL.

Definition at line 532 of file cdr.c.

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void cdr_set_ext_bnd ( cdr_grid_t * grid )

void cdr_set_ext_bnd_r ( cdr_grid_t * grid )

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void cdr_calc_d_dens ( cdr_grid_t * grid )

Calculates the derivatives of the densities for each point of the grid.

Definition at line 830 of file cdr.c.

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void cdr_calc_d_dens_r ( cdr_grid_t * grid )

void cdr_advect_diffu ( cdr_grid_t * grid )

Adds the advection and diffusion terms to the derivatives of the densities.

Definition at line 900 of file cdr.c.

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void cdr_advect_diffu_r ( cdr_grid_t * grid )

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double cdr_courant ( cdr_grid_t * grid )

Returns the minimum tau that satisfies the Courant-Friedrichs-Lewy restriction (CFL).

Definition at line 971 of file cdr.c.

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void cdr_update	(	cdr_grid_t *	orig,
		cdr_grid_t *	dest,
		double	h
	)

Writes into the densities of the grid dest the densities of grid orig plus its derivatives times h.

If orig = dest, this implements an Euler step. But it can also be used as a tool to implement a RK

Definition at line 1075 of file cdr.c.

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void cdr_rk2_update	(	cdr_grid_t *	dens_0,
		cdr_grid_t *	d_dens_1,
		cdr_grid_t *	d_dens_2,
		cdr_grid_t *	dest,
		double	h
	)

Sets dest->dens = dens_0->dens + h/2 * d_dens_1->d_dens +
h/2 * d_dens_2->d_dens.

Useful to implement 2nd order RK time-stepping.

Definition at line 1107 of file cdr.c.

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void cdr_rk2_update_r	(	cdr_grid_t *	dens_0,
		cdr_grid_t *	d_dens_1,
		cdr_grid_t *	d_dens_2,
		cdr_grid_t *	dest,
		double	h
	)

Recursive version of cdr_rk2_update.

Note: we assume here that all the trees are congruent: this is, they have the same structure with nodes of the same size.

Definition at line 1143 of file cdr.c.

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void cdr_self_update_r	(	cdr_grid_t *	grid,
		double	h
	)

Recursive version of the former QQQQ, used to implement Euler integration.

Definition at line 1168 of file cdr.c.

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void cdr_like_update_ar	(	cdr_grid_t *	grid,
		cdr_grid_t *	new_grid,
		double	h
	)

Yet another recursive version of cdr_update, used to implement higher order Runge-Kutta integrations.

It creates a new tree of cdr grids.

Definition at line 1184 of file cdr.c.

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double cdr_rk2	(	cdr_grid_t *	grid,
		double	h,
		double	t
	)

Computes the grid error. QQQQ.

Recursive version of cdr_grid_error. QQQQ Makes a full second order Runge-Kutta step.

Returns the timestep actually performed, which can be smaller that h if it does not satisfy the Courant criterium.

Definition at line 1262 of file cdr.c.

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void cdr_update_refined ( cdr_grid_t ** ptree )

Takes a pointer to a family of cdr grids, creates a new family which is stored in that pointer and takes rid of the initial family.

This function is the entry point of the refinement code.

Definition at line 1363 of file cdr.c.

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void cdr_calc_maxs ( cdr_grid_t * grid )

Updates the values of max_dens and max_charge.

This values are needed for the refinement criterium.

Definition at line 1383 of file cdr.c.

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void cdr_refine ( cdr_grid_t * grid )

Uses the previous routines to refine (if needed) a cdr grid.

Definition at line 1626 of file cdr.c.

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void cdr_refine_r	(	cdr_grid_t *	grid,
		cdr_grid_t *	source
	)

Recursively refines a cdr grid and constructs a tree based on it.

if source == NULL
then uses the initial densities
else sets the densities of the newly created grids by interpolating and copying from the tree source.

Definition at line 1720 of file cdr.c.

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void cdr_match_r	(	cdr_grid_t *	grid1,
		cdr_grid_t *	grid2
	)

Examines pairs of grids and matches them and all their descendants.

If grid2 == NULL, matches only the descendats of grid1. Hence, this routine is usually called as cdr_match_r (root, NULL).

Definition at line 1763 of file cdr.c.

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void cdr_set_bnd ( cdr_grid_t * grid )

Sets the boundary conditions of all children of grid by interpolating from grid itself.

Definition at line 1888 of file cdr.c.

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void cdr_set_bnd_r ( cdr_grid_t * grid )

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void cdr_restrict ( cdr_grid_t * grid )

Restricts a grid with all its children.

Definition at line 2083 of file cdr.c.

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void cdr_restrict_r ( cdr_grid_t * grid )

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void cdr_set_dens	(	cdr_grid_t *	cdr,
		int	species,
		int	mode,
		double	factor,
		double(*)(double, double, double)	f
	)

Sets the densities of species species according to the function $f (x, y, z)$ .

mode can be one of the following:
SET_DENS_OVERWRITE: Set the dens to f(x, y, x), ignoring what was there before.
SET_DENS_ADD: Adds f to the former density.
SET_DENS_SUB: Substracts f from the former density.

Definition at line 2126 of file cdr.c.

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void cdr_init_dens ( cdr_grid_t * cdr )

Inits the densities of all species.

Definition at line 2173 of file cdr.c.

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cdr_grid_t* cdr_scratch_init ( void )

Initializes the densities allocating a new grid family.

Definition at line 2197 of file cdr.c.

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mapper_t** cdr_mappers_a ( interpol_method_t * interp_method )

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void cdr_free_mappers ( mapper_t ** mappers )

Frees the memory of all mappers QQQQ.

Definition at line 1988 of file cdr.c.

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void cdr_dump	(	cdr_grid_t *	grid,
		const char *	prefix,
		const char *	name
	)

Dumps all the contents of the given grid into filenames given by prefix and name.

Definition at line 2226 of file cdr.c.

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void cdr_dump_r	(	cdr_grid_t *	grid,
		const char *	prefix,
		const char *	name,
		FILE *	infp,
		double	sim_time
	)

Dumps all the contents of the given grid into filenames given by prefix and name.

It also writes in tree.NAME.dat the tree structure of grid, in a format appropiate for cdr_load_tree to understand.

infp has to be NULL when called from outside.

The format of a tree.NAME.dat is as follows. Each line is composed by a "command" and some parameters. the "commands" can be

time parameter: sim_time Writes the current simulation time, as received in sim_time

open parameters: gridname r0 z0 r1 z1 level ext_bound margin

Reads the densities from the files given by gridname, with the corresponding values of the grid parameters. Leaves the grid open to add childrens to it. Those children will be all the grids read until the grid is closed.

close parameters: gridname

Closes the latest opened grid. All subsequent grids will be regarded as brothers of gridname.

Definition at line 2360 of file cdr.c.

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cdr_grid_t* cdr_load_tree_r	(	const char *	prefix,
		const char *	name,
		FILE *	infp
	)

Reads the data format produced by cdr_dump_r and creates a complete tree from it.

This function is really quick-and-dirty: one should check the fscanfs and do everything cleanlier.

Definition at line 2425 of file cdr.c.

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void cdr_dump_frames	(	cdr_grid_t *	grid,
		const char *	prefix,
		const char *	name
	)

Given a grid family, writes in the file named fname the coordinates of the frames that define the grid and his descendants.

Definition at line 2511 of file cdr.c.

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void pois_init ( void )

All initialization of the Poisson solver has to be here.

Definition at line 86 of file poisson.c.

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pois_grid_t* pois_new_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1
	)

Creates a 2D Poisson grid.

Definition at line 109 of file poisson.c.

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pois_grid_t* pois_new_3d_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1,
		int	ntheta
	)

Creates a new 3D Poisson grid.

r0, z0, r1, z1 are in GRID units

Definition at line 123 of file poisson.c.

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void pois_free ( pois_grid_t * grid )

Frees the memory allocated by pois_new_a.

Definition at line 163 of file poisson.c.

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void pois_free_r ( pois_grid_t * grid )

Recursively frees a tree of Poisson grids.

Definition at line 180 of file poisson.c.

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pois_grid_t* pois_new_glob_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1,
		int	level
	)

Creates a new Poisson grid.

r0, r1... are in global units (i.e. independent of the grid level).

Definition at line 196 of file poisson.c.

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pois_grid_t* pois_init_tree_a	(	int	r0,
		int	z0,
		int	r1,
		int	z1
	)

Starts the tree of Poisson grids with the two coarsest ones.

Receives the grid dimensions at level 0.

Definition at line 217 of file poisson.c.

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REAL* pois_boundary_a	(	pois_grid_t *	grid,
		int	boundary
	)

Is it possible to use a single function to handle all four boundaries?

Maybe this should be rewritten to use the interpol2 module?

Definition at line 244 of file poisson.c.

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void pois_solve_grid	(	pois_grid_t *	grid,
		pois_problem_t *	prob,
		double	lambda,
		double	s
	)

Solves the Poisson equation, calling the FISHPACK routine.

Assumes that grid->charge is already set.

Definition at line 334 of file poisson.c.

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void pois_set_phi_boundaries	(	pois_grid_t *	grid,
		REAL *	boundaries[],
		int	left_neu,
		int	right_neu,
		int	bottom_neu,
		int	top_neu
	)

Uses the boundaries[] vectors to set the boundaries by interpolation for the phi array of a grid.

(in the extra space we allocated when we created the array). xxx_neu tells us if the xxx boundary has Neumann b.c. (or unspecified, as FISHPACK calls them if they are applied in the axis)

TODO: Please rewrite this mess.

Definition at line 465 of file poisson.c.

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int pois_map_charge	(	pois_grid_t *	pois,
		cdr_grid_t *	cdr,
		int	mode
	)

void pois_set_error ( pois_grid_t * grid )

Estimates the error on this grid by comparing with the calculations for his parent and performing a Richardson extrapolation.

Definition at line 561 of file poisson.c.

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int pois_refine	(	pois_grid_t *	grid,
		double	threshold
	)

The refinement routine.

Threshold is initially pois_max_error, but if we get too large refinement it can be increased (after warning the user that we are not reaching the accuracy that he asked for).

Definition at line 606 of file poisson.c.

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pois_grid_t** pois_solve_a	(	cdr_grid_t *	cdr,
		pois_problem_t *	prob
	)

Takes a cdr tree and solves the Poisson equation for it.

Returns a poisson tree.

Definition at line 763 of file poisson.c.

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pois_grid_t** pois_gen_solve_a	(	cdr_grid_t *	cdr,
		pois_problem_t *	prob,
		mapper_t **	mappers,
		double	es
	)

Solves a Poisson/Helmholtz equation with FISHPACK and maps the result using a given set of mapper.

From this method downwards (in the sense of calling order, not file organization), all the code is shared by the Poisson solver and the Photoionization (Helmholtz) solver.

Definition at line 777 of file poisson.c.

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pois_grid_t* pois_solve_mode	(	cdr_grid_t *	tree,
		cdr_grid_t *	cdr,
		pois_problem_t *	prob,
		int	mode,
		double	es
	)

Solves a single Fourier mode.

tree is the root of the cdr tree with extra_pois_levels added. cdr is the cdr grid at level 0, contained in tree:

cdr = tree->first_child->firts_child...->first_child _________ extra_pois_levels __________/

Definition at line 836 of file poisson.c.

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void pois_solve_r	(	pois_grid_t *	pois,
		cdr_grid_t *	cdr,
		pois_problem_t *	prob,
		int	mode,
		double	es,
		double	threshold
	)

Recursively solves one Poisson grid.

Definition at line 866 of file poisson.c.

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double pois_phi_at	(	pois_grid_t *	grid,
		double	r,
		double	z,
		double	theta
	)

Finds the best-possible approximation for the potential at a given point (r, z, theta) by interpolating from the finest grid that covers that point.

Definition at line 1452 of file poisson.c.

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void pois_dump	(	pois_grid_t *	grid,
		const char *	prefix,
		const char *	name
	)

Dumps all the contents of the given grid into filenames given by prefix and name.

Definition at line 1507 of file poisson.c.

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void pois_dump_r	(	pois_grid_t *	grid,
		const char *	prefix,
		const char *	name
	)

Dumps all the contents of the given grid into filenames given by prefix and name.

Definition at line 1540 of file poisson.c.

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void pois_write_error_r	(	pois_grid_t *	grid,
		FILE *	fp
	)

Writes some error measures of this grid and its descendants into fp.

Definition at line 743 of file poisson.c.

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void pois_error_measures	(	pois_grid_t *	grid,
		double *	L1,
		double *	L2,
		double *	Lmax
	)

Calculates the error measure of this grid.

For debug/testing purposes

Definition at line 717 of file poisson.c.

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void pois_inhom_init ( void )

pois_inhom_init QQQQ

Definition at line 939 of file poisson.c.

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double pois_inhom_phi	(	double	r,
		double	z
	)

Returns the potential created by a unit charge located at pois_inhom_z between an electrode at 0 and a second one at pois_inhom_L.

Definition at line 1025 of file poisson.c.

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double pois_inhom_er	(	double	r,
		double	z
	)

Radial component of the field.

Definition at line 1036 of file poisson.c.

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double pois_inhom_ez	(	double	r,
		double	z
	)

Axial component of the field.

Definition at line 1047 of file poisson.c.

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double pois_inhom_q_factor ( pois_grid_t * pois )

Once we have the electrostatic potential created by the space charges, we use this function to compute the multiplying factor of the floating charge.

One can also forget about keeping the potential fixed somewhere and impose a constant (non-floating, but may depend on time) charge pois_inhom_fixed_q, which is used if nonzero. The use of that is to simulate a charged cloud close to the earth, which acts as an electrode: usually you would also combine that with the sprite module, that allows varing neutral densities.

Definition at line 1067 of file poisson.c.

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void pois_add_inhom_phi_r	(	pois_grid_t *	grid,
		double	q
	)

Adds the potential created by the needle to a Poisson grid and their descendants.

Note that $\phi$ here is in Fourier space and the Laplacian potential is always axi-symmetric, so you only have to call this function with the zero-mode of the Poisson grids.

The reason that it is better to add the inhomogeneous field to the potential and not later to the electric fields is that if we do that, we will have to substract two large and very curved functions that give something close to zero: the error we make then will be comparable to the result.

Definition at line 1101 of file poisson.c.

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void photo_init ( )

Initializes photoionization QQQQ?

Definition at line 48 of file photo.c.

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void photo_register	(	double	A,
		double	lambda
	)

Registers a photoionization term with given A and lambda.

Definition at line 174 of file photo.c.

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void photo_copy_list	(	photo_term_t *	src,
		photo_term_t **	dest
	)

Copies a list of photo terms into *dest.

Definition at line 189 of file photo.c.

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void photo_unregister_all ( void )

Unregisters all the photoionization terms and frees the allocated space.

Definition at line 218 of file photo.c.

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void photo_dft_r	(	cdr_grid_t *	grid,
		int	sign
	)

Transforms back the photoionization calculation into real space.

Definition at line 232 of file photo.c.

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void photo_copy_source ( cdr_grid_t * grid )

Copies the derivative of the ion density into cdr->charge.

The ion density, which is supposed to be at this point, the impact ionization) into cdr->charge, which will be used as the source for the Poisson/Helmholtz solver.

Definition at line 252 of file photo.c.

void photo_add_term	(	photo_term_t *	term,
		cdr_grid_t *	cdr
	)

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void photo_add_term_r	(	photo_term_t *	term,
		cdr_grid_t *	cdr
	)

...and the recursive version of photo_add_term

Definition at line 301 of file photo.c.

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pois_grid_t** photo_calc_term	(	photo_term_t *	term,
		cdr_grid_t *	cdr,
		int	i
	)

photo_calc_term QQQQ

Definition at line 314 of file photo.c.

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void photo_calc	(	photo_term_t *	terms,
		cdr_grid_t *	cdr
	)

Calculates the photoionization and adds it to the derivatives of the species densities.

Definition at line 327 of file photo.c.

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void photo_load_file ( char * fname )

Loads a photoionization file, consisting in a series of rows with A and lambda.

Definition at line 365 of file photo.c.

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void init_parameters ( void )

Initializes the parameters.

The global parameters will get their default values. These values correspond with the values in input/defaults.cfg

Definition at line 54 of file cstream.c.

void cstream_init ( void )

Here all the initialization calls.

Definition at line 364 of file cstream.c.

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void cstream_end ( void )

Here all the cleaning and finishing calls.

Definition at line 388 of file cstream.c.

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void cstream_set_field_at_time ( double t )

When we use a time-varying external field, we update the field components at each timesteps.

Definition at line 400 of file cstream.c.

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void dft_transform	(	rz_array_t *	in,
		rz_array_t *	out,
		int	sign
	)

Transform the discrete fourier transformations ????

Definition at line 37 of file dft.c.

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void dft_diff	(	grid_t *	grid,
		rz_array_t *	f
	)

Calculates the Fourier transform of the derivative of a function given its Fourier transform.

Definition at line 97 of file dft.c.

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void dft_weight	(	cdr_grid_t *	cdr,
		rz_array_t *	var,
		double	weights[],
		double	power
	)

Calculates the weight for a given cdr grid and a variable ???

For a given cdr grid and a variable, calculates its "weight": the integral of the variable raised to power for each Fourier mode. weights[] must be able to contain at least cdr->ntheta values.

Definition at line 143 of file dft.c.

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void dft_out_weights	(	cdr_grid_t *	grid,
		const char *	prefix,
		double	t
	)

Outputs to a file 'weights.tsv' the results of dft_weight.

Assumes that grid->charge is calculated but in real space then it transforms it to Fourier space and leaves it like that: so do not assume that grid->charge is unchanged.

grid->dens[electrons], on the other hand, is transformed forth and back.

Definition at line 177 of file dft.c.

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void dft_perturb	(	cdr_grid_t *	cdr,
		rz_array_t *	var,
		double *	epsilon_k
	)

Perturbs a FFT-transformed variable.

Assumes that the unperturbed variable is axi-symmetrical and hence all modes are zero except k=0. The perturbation is then selected as a Gaussian random number epsilon_k times the zero-mode value of the variable. epsilon_k is distributed as epsilon_k = N(0, perturb_epsilon).

Definition at line 246 of file dft.c.

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void dft_dens_perturb_r	(	cdr_grid_t *	grid,
		int	species,
		double *	epsilon_k
	)

Takes a density in real space, transforms it to Fourier space, perturbs it and then transforms back to real space.

Definition at line 270 of file dft.c.

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int find_species_by_name ( const char * spec_name )

Returns the position in the species-array of a given species.

Returns -1 if not found.

Definition at line 28 of file reaction.c.

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void react_add ( reaction_t * react )

Adds a given reaction to the reaction list.

Definition at line 48 of file reaction.c.

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void react_init ( )

Initializes the list of reactions.

Definition at line 221 of file reaction.c.

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void react_apply_r	(	reaction_t *	react,
		cdr_grid_t *	grid,
		int	overwrite
	)

Recursive version of react_apply.

Definition at line 167 of file reaction.c.

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void react_apply_all ( cdr_grid_t * grid )

Applies all reactions to the given grid and his descendants.

Definition at line 192 of file reaction.c.

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void kinetic_init ( void )

Any initialization required by the kinetic model, has to be done in this function.

Definition at line 31 of file rt.c.

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double spr_density_at ( double altitude )

The density at a given height, assuming dens = 1.0 at height = 0.0.

We are assuming an exponential profile here but in principle any other profile would also do.

Definition at line 36 of file sprites.c.

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void spr_init ( )

Initialize the sprite module.

We have to remember the values of the global variables that we will adapt to altitude.

Definition at line 48 of file sprites.c.

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void spr_hook ( cdr_grid_t * grid )

Hook to update the variables that depend on the head altitude.

Has to be called AFTER the charge is calculated.

Definition at line 65 of file sprites.c.

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void spr_update ( double altitude )

Updates the magnitudes that we are tracking according to a given altitude.

Definition at line 78 of file sprites.c.

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double spr_head_altitude	(	cdr_grid_t *	grid,
		int	sign
	)

Finds the position of the streamer head by locating the maximum (or -maximum) of the charge along the streamer axis.

sign has to be +1 for positive streamers and -1 for negative streamers.

Definition at line 101 of file sprites.c.

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void read_input_file	(	const char *	f_kinetic_name,
		const char *	filename
	)

Reads the kinetic parameters (species, reactions) from file filename.

Definition at line 55 of file rt.c.

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