# If 0, do full 3D; for any other value, do {x,y} to r (effectively 2D).
do_xy_to_r		0

############################################################
## Time step and number of steps.                         ##
############################################################
timestep	0.0001
run		1
outputFrequency 200

############################################################
## Spatial domain (length is in MICROMETERS).             ##
############################################################
Lx	2.0
Ly	2.0
Lz	2.0
Nx	71
Ny	71
Nz	71

############################################################
## Equation parameters.                                   ##
############################################################
DiffusionCoefficient	1.0
Intensity_I_0		10.0
Reactivty_kh		1.0

############################################################
## Initial conditions. p(r,t=0) = p0.                     ##
############################################################
p0			1.0

############################################################
## Name of the output file for the observable.            ##
############################################################
ObsFName		/home/anton/plugins/fmtool/test/3D.dat
# Should we write the 3D map of the PSF in a .dx file?
# Set 0 for no writing, any other value for writing.
PSF_write_dx		5

############################################################
## Point spread function.                                 ##
############################################################
# Type of PSF: 0 for spherical, 1 for rectangular; any other value - read from the file.
TypePSF			5
# Center of the PSF.
x0_PSF			0.0
y0_PSF			0.0
z0_PSF			0.0
# Radius for the spherical PSF.
R_PSF			0.26
# Size for the rectangular PSF.
LPSF_x			0.2
LPSF_y			0.2
LPSF_z			0.2

############################################################
## For reading the PSF from the file.                     ##
############################################################
# Type of microscopy: 0 for confocal, 1 for 4Pi, any other positive value for multiple beams.
MS_type			5

# Illumination mode: 0 for one-photon, any other value for two-photon.
mode_ill		5

# Illumination angle alpha (degrees).
alpha_ill		68.5
# PSF files corresponding to the illumination angle alpha.
PSF_ill_fname		/Projects/anton/FRAP/Ifunctions/68.5
# Refraction index for the illumination.
n_ill			1.46
# Wavelength for the illumination (NANOMETERS).
lambda_ill		910.0
# Angle phi (degrees).
phi_ill			90.0

# Detection angle alpha (degrees).
alpha_det		68.5
# PSF files corresponding to the detection angle alpha.
PSF_det_fname		/Projects/anton/FRAP/Ifunctions/68.5
# Refraction index for the detection.
n_det			1.46
# Wavelength for the detection (NANOMETERS).
lambda_det		530.0

############################################################
## PSF given by the interference of several beams         ##
############################################################
# How many beams one should use.
N_beam			16
# Vectors k and e_x for all beams.
# Format: "a1 a2 a3 a4", where a1 is the serial number if the beam,
# and a2 a3 a4 are the x, y, and z components of the vector.
k_beam		1 0.0 0.0 -1.0
e_x_beam	1 1.0 0.0 0.0
k_beam		2 0.0 0.0 1.0
e_x_beam	2 1.0 0.0 0.0
k_beam		3 0.0 1.0 0.0
e_x_beam	3 1.0 0.0 0.0
k_beam		4 0.0 -1.0 0.0
e_x_beam	4 1.0 0.0 0.0
k_beam		5 0.0 1.0 1.0
e_x_beam	5 1.0 0.0 0.0
k_beam		6 0.0 -1.0 -1.0
e_x_beam	6 1.0 0.0 0.0
k_beam		7 0.0 1.0 -1.0
e_x_beam	7 1.0 0.0 0.0
k_beam		8 0.0 -1.0 1.0
e_x_beam	8 1.0 0.0 0.0
k_beam		9 0.0 1.0 0.5
e_x_beam	9 1.0 0.0 0.0
k_beam		10 0.0 0.5 1.0
e_x_beam	10 1.0 0.0 0.0
k_beam		11 0.0 -0.5 1.0
e_x_beam	11 1.0 0.0 0.0
k_beam		12 0.0 -1.0 0.5
e_x_beam	12 1.0 0.0 0.0
k_beam		13 0.0 -0.5 -1.0
e_x_beam	13 1.0 0.0 0.0
k_beam		14 0.0 -1.0 -0.5
e_x_beam	14 1.0 0.0 0.0
k_beam		15 0.0 0.5 -1.0
e_x_beam	15 1.0 0.0 0.0
k_beam		16 0.0 1.0 -0.5
e_x_beam	16 1.0 0.0 0.0