Milne-Eddington inversion code

Milne-Eddington inversion code (https://github.com/HaoLi-70/Milne-Eddington/) An example demonstrating the use of GST/NIRIS data has been added to the Github repository. --- Overview A pixel-by-pixel Stokes inversion code, written in C and paralleled with MPI, follows the analytic solutions described in J. C. del Toro Iniesta (2003) and E. Landi Degl’Innocenti & M. Landolfi (2004). The Levenberg–Marquardt method is used to solve the nonlinear least-squares problem. Geometry The direction of positive Stokes U corresponds to a counterclockwise rotation of 45$^\circ$ with respect to that of positive Stokes Q, while Stokes V represents the difference between the right- and left-handed circular polarization. The observer is suppose to face the radiation source. Parameters The inverted inclination angle ($\theta_B$) is defined as the angle between the magnetic field vector and the direction pointing to the observer, and the azimuth angle ($\phi_B$) is the counterclockwise from direction of positive Stokes Q. The code adopts the sum ($S$ = $S_0$ + $S_1$) and a ratio $\beta$ = $S_0$/($S_0$ + $S_1$) instead of the source function ($S_0$) and its gradient ($S_1$), since S corresponds to the continuum intensity, which is uncorrelated with other parameters. In addition, a folded boundary condition was applied to $\phi_B$ to prevent solutions from becoming trapped at the bounds. --- Requirements C/C++ compiler [CFITSIO](https://heasarc.gsfc.nasa.gov/docs/software/fitsio/) library (for FITS file input/output) MPI library (for parallel execution) Make / GNU Make --- Installation Clone the repository and build the program: ``` git clone https://github.com/HaoLi-70/Milne-Eddington.gitcd Milne-Eddington./configure --hardmake``` --- Example ```cd niris_examplempirun -np 4 ../MEINV``` --- Input/Output Input: niris_example.fits: FITS file [nl,4,nx,ny] containing the Stokes profiles. niriswavelength.fits: FITS file [nl] containing the wavelength. input: control file. Output: res.fits: FITS file [10,nx,ny] containg the inverted model parameters ($B$, $\theta_B$, $\phi_B$, $v_{\rm los}$, $\rm \Delta\lambda_D$, $a$, $\eta$, $S$, $\beta$) and the $\chi^2$. ---