ConfigurationΒΆ
The code is controlled by a single human-readable configuration file.
In order to use this option, you need to have the configparser
package installed in your system. It can be downloaded from
http://www.voidspace.org.uk/python/configobj.html or installed as a standard
Python package using ``pip install configparser’‘. The serial version of the code
is run using:
./run.py conf.ini
and the parallel code is run with
./run.py conf.ini nProcessors
An example of the file, that is self-explanatory, is:
# Hazel configuration File
#####################
# General information
#####################
[Files]
Input model file = 'ATOMS/helium.mod'
File with observations = 'OBSERVATION/test_2comp.prof'
File with inverted profiles = 'test.inversion'
File with inverted parameters = 'test.parameters'
[Working mode]
Action = 'inversion' # 'synthesis' or 'inversion'
Verbose = no
Linear system solver = 'LU' # 'LU' or 'CG'
Stopping volume for DIRECT = 0.001
[General parameters]
Synthesis mode = 'exact' # 'thin' or 'exact'
Include stimulated emission = yes
Include magnetic field = yes
Include Paschen-Back effect = yes
Include atomic level polarization = yes
Include magneto-optical effects in the RT = yes
Include stimulated emission in the RT = yes
Multiplet = 10830 # 10830, 5876, 7065, 3889 A
Line-of-sight angles = 0.0, 0.0, 90.0 # theta, chi, gamma deg
Wavelength axis = -3.0, 2.5, 200 # Minimum, maximum and number of grid points
#####################
# Synthesis parameters
#####################
[Synthesis]
Number of slabs = '1' # '1' -> single slab, '1+1' -> two slabs with same field, '1+1B' -> 2 slabs with different field, '2' -> two slabs added with a filling factor
Boundary condition = 4.098e-5, 0.0, 0.0, 0.0 # I0, Q0, U0, V0. It can also be a file that contains the boundary condition vs wavelength (see boundary.dat in run directory)
a = 0.0
height = 3.0 # Real height if positive, apparent height if negative arcsec
ff = 0.0
[[Slab 1]]
B = 0.0 # G
thetaB = 0.0 # deg
chiB = 0.0 # deg
vdopp = 8.0 # km/s
tau = 1.0
vmac = 0.0 # Positive is redshift km/s
beta = 1.0
[[Slab 2]]
B = 0.0 # G
thetaB = 0.0 # deg
chiB = 0.0 # deg
vdopp = 0.0 # km/s
tau = 0.0
vmac = 0.0 # Positive is redshift km/s
beta = 1.0
#####################
# Ranges for the DIRECT method [min, max]
#####################
[Ranges]
a = 0,0.5
ff = 0.0,1.0
[[Slab 1]]
B = 800,1100
thetaB = 0,180
chiB = 0,180
vdopp = 2,12
tau = 0.1,2
vmac = -5,5
beta = 0.5,2
[[Slab 2]]
B = 800,1100
thetaB = 0,180
chiB = 0,180
vdopp = 2,12
tau = 0.1,2
vmac = -5,5
beta = 0.5,2
#####################
# Parameters to invert
#####################
[Inversion]
Iterations in LM = 20
Number of cycles = 4
Inversion modes = 'DIRECT', 'LM', 'DIRECT', 'LM' # 'DIRECT' for DIRECT algorithm and 'LM' for Levenberg-Marquardt
[[Cycles]]
a = 1, 1, 0, 0
ff = 0, 0, 0, 0
[[[Slab 1]]]
B = 0, 0, 1, 1
thetaB = 0, 0, 1, 1
chiB = 0, 0, 1, 1
vdopp = 1, 1, 0, 0
tau = 1, 1, 0, 0
vmac = 1, 1, 0, 0
beta = 0, 0, 0, 0
[[[Slab 2]]]
B = 0, 0, 0, 0
thetaB = 0, 0, 0, 0
chiB = 0, 0, 0, 0
vdopp = 0, 0, 0, 0
tau = 0, 0, 0, 0
vmac = 0, 0, 0, 0
beta = 0, 0, 0, 0
[[Weights]]
Stokes I = 1.0, 1.0, 1.0, 1.0
Stokes Q = 0.0, 0.0, 1.0, 1.0
Stokes U = 0.0, 0.0, 1.0, 1.0
Stokes V = 0.0, 0.0, 1.0, 1.0
The code will convolve with a spectral point spread function if a file called psf.txt is placed on the
directory where you run the code. This file contains a first line with the number of points of the PSF.
Then a single column giving the transmission in a wavelength axis with a step equal to that of the observations.
If this file is not present, no convolution will be done.