#!/usr/bin/env jabs

#This is a comment

set ion 4He #4He is also known as "a"

set energy 2027keV

set alpha 0 #this and the following two lines are equivalent

set alpha 0deg

set alpha "0 deg"

#Default cross sections can be changed easily between the built-in models, see other examples on how to define reactions using e.g. R33 files

#set cs_rbs Rutherford

#RBS (and ERD) reactions are added automatically when running a simulation or a fit, if no reactions are specified

#load reactions RBS

#add reaction RBS 197Au

set fluence 2.0e13 #Fluence is actually total number of ions, not ions/cm2... this should *not* be multiplied by detector solid angle (JaBS will do that)

load exp "experimental.dat"

#sample can be set with one command

#This will add gamma roughness in the Au layer using 20 subspectra in simulation (default, so it could be omitted)

set sample Au 30tfu rough 20tfu n_rough 20 SiO2 6500tfu Si 20000tfu

#or loaded from a file (tabular data)

#load sample "sample.txt"

load script "detector.jbs" #Scripts can be loaded (run). It is convenient to store detector in a separate script.

#The following line can be uncommented after this script is run. We save the detector calibration at the end of the script.

#load script "calibration_out.jbs"

set emin 150keV #Speed up by setting the minimum energy in the simulation (optional)

#show sim

simulate #Run a simulation

save spectra "simulated_out.csv" #Save spectra

#fit ranges (channels) must be specified before fitting. We can define multiple ranges with one command.

add fit range [200:449] [450:700]

add fit range [1050:1110]

#Number of iterations can be limited if there is reason to suspect the fit won't converge...

#set maxiter 100

#Run a fit

fit *calib*,fluence,thick1,thick2,rough1,conc2_O

save spectra "example_out.csv"

save calibration "calibration_out.jbs" #detector calibration can be saved to a script file. This can be loaded back in.

save sample "sample_out.txt" #fitted sample can be saved (and loaded back in later!)

#show detector

#show fit

#show fit correlation

#show sample profile

show fit ranges

#roi [1060:1092]