ART - Advanced Radiative Transfer code

LTE RT code for solar ALMA applications (Formerly known as RTma.)

Installation

To run & compile, you will need C++ & Fortran compiler with MPI. Additional that you will need a parallel version of the HDF5 library. On MacOS (M1, or Intel) the easiest is to install all requirements via Home Brew. You will need the following packages:

brew install gcc openmpi hdf5-mpi

On Linux machine @ITA you most likely have all necessary compilers and libraries installed, and you just need to load the right modules (see compilation section).

Compilation

To compile, enter the src subfolder and type make MACHINE=xxx, where xxx is the file's name from the machine subfolder. These files are for machine-specific setup (compilers, flags etc.). You might want to create a new one for your own machine (host) or use an existing one. For example, if you have installed gcc & openmpi on Mac Os through Home Brew you can simply use:

make MACHINE=mac_gnu

Successful installation should generate RTma.x executable:

...
mpicxx -O2 -mtune=native -std=c++11 -I/opt/homebrew/include/ -g  -c main.cc -o main.o
mpicxx  -o RTma.x cop.o  eoswrap.o witt.o model.o io.o clte.o main.o -lstdc++ -lc++ -L/opt/homebrew/lib -lhdf5 -lhdf5_hl

Input files

To run ART you need an input atmosphere in *.h5 (HDF5) format. In the example folder you can find a small model with following structure:

h5ls model.h5

dens                     Dataset {1, 25, 15, 269}
dx                       Dataset {15}
dy                       Dataset {25}
temperature              Dataset {1, 25, 15, 269}
xne                      Dataset {1, 25, 15, 269}
z                        Dataset {1, 25, 15, 269}

Where:

* `dens` - is density in CGS units
* `dx`,`dy` - mesh spacing in the X-Y direction
* temperature - ..well obvious but make sure it is in [K]
* xne - electron density in CGS [ 1/cm^3 ]
* z - z-axis spacing in [cm]

There is also an example of a python script for generating input models from Bifrost snapshots in raw format (or official FITS) in utils.

Input file with frequencies

Additional to the input model atmosphere, you will also need an input file to define a list of frequencies for which you wish to calculate intensities. Example of such file (you can use it for template) can be also found in example folder.

# well obvious ..input and out files 
input_model = model.h5
output_profiles = synthetic.h5

# do not touch 
lines_file = lines.vald.input
rt_solver = 0
verbose = 1
mu = 1.0

# EOS can be witt (default) or pisk (slower)
eos = witt

# Cut the model from above until T = temperature_cut
temperature_cut = 50000.0
		
# Compute contribution function (default = 0)
get_contribution_funtion = 0


# Options (stderr, stdout, master, file, null)
logfile = master

# Finally, a list of frequencies.. wavelengths in Angstrom units // first is ~1 mm, and second ~3.1 mm
region = 10000000., 1.0, 1, 1.0, none, none
region = 31000000., 1.0, 1, 1.0, none, none
region = 6300.000, 0.01, 16, 1.0, none, none
region = 5000.000, 1.0, 1, 1.0, none, none

Running ART

Ok, we have the model and input file.. to run use mpirun

cd example
mpirun -np 4 ./RTma.x -i input.cfg

expected output:

➜ mpirun -np 4 ./RTma.x -i input.cfg

Using input file: input.cfg
info: readInput: input_model -> model.h5
info: readInput: output_profiles -> synthetic.h5
info: readInput: lines_file -> lines.vald.input
info: readInput: rt_solver -> 0
info: readInput: verbose -> 1
info: readInput: mu -> 1.0
info: readInput: eos -> witt
info: readInput: temperature_cut -> 50000.0
info: readInput: get_contribution_funtion -> 0
log target 0x20952b978
info: readInput: region -> 10000000.,1.0,1,1.0,none,none
info: readInput: region -> 31000000.,1.0,1,1.0,none,none
info: readInput: region -> 6300.000,0.01,16,1.0,none,none
info: readInput: region -> 5000.000,1.0,1,1.0,none,none
log target 0x20952cda8
log target 0x20952cda8
log target 0x20952cda8
test log 0/4
info: io, read_lines: read [3] lines
info: initReadIO: Found dims [ nt=1, ny=25, nx=15, ndep=269 ]
info: initReadIO: Found vars [ z ][ temperature ][ dens ][ xne ]
info: processing 100%

Output file

After a successful run you should get an HDF5 under the name you set in the input file ( synthetic.h5 in the example ) with the following structure:

➜ h5ls synthetic.h5

Stokes_I                 Dataset {1, 25, 15, 19}
Tau1                     Dataset {1, 25, 15, 19}
Wavelength               Dataset {19}

Where:

*  `Stokes_I` - Calculated intensities, the first dimension is time (not used), then `x`,`y` and `wavelength`.
*  `Wavelength` - is the axis for 4th dimension (list of wavelengths in Angstroms) 
*  `Tau1` - is formation hight in `cm` i.e., value on `z-axis`  where `Tau_{wavelenght} ~= 1.0`.

These should be easy to plot via Python // see example folder again.