Strömgen Sphere example in 3D
-----------------------------

This directory contains two examples in one:

    -   run a Strömgren sphere example, where a single central
        star ionizes the surrounding medium in a box.
        To run this example, use the provided `run.sh` script.
        This script will then make use of the `makeIC.py` and
        `plotSolution.py` script.

        There are a few variations:
    
        - `run_singlebin.sh`: single-frequency-bin static fixed 
        temperature Stromgren Sphere with pure hydrogen. This 
        script will make use of `makeIC.py` and 
        `plotStromgren3DsinglebinCheck.py`, plotting the neutral 
        fraction against an analytic solution.

        - `run_MF.sh`: multifrequency static variable temperature 
        Stromgren Sphere with pure hydrogen. This script will make 
        use of `makeIC.py` and `plotStromgren3DMFCheck.py`, comparing 
        the neutral fraction and temperature with published solutions.

        - `run_MFHHe.sh`: multifrequency static variable temperature 
        Stromgren Sphere with hydrogen (75%) and helium (25%). This 
        script will make use of `makeIC_HHe.py` and 
        `plotStromgren3DMFHHeCheck.py`, comparing the neutral fraction 
        and temperature with published solutions. 


    -   run a propagation test of photons emitted from a single 
        central source in an otherwise uniform box.
        To run this example, use the provided `runPropagationTest.sh` script.
        This script will then make use of the `makePropagationTestIC.py` and
        `plotPhotonPropagationCheck.py` script.


Additional scripts:
    -   `plotRadiationProjection.py`: Plots a projection of the radiation
        quantities (energies, fluxes). NOTE: you might need to change the
        'snapshot_base' variable at the top of the script depending on which
        solutions you want to plot.
             

To use the GEAR RT model, compile with :
for the propagation test and the "singlebin" test:
    --with-rt=GEAR_1 --with-rt-riemann-solver=GLF --with-hydro=gizmo-mfv --with-riemann-solver=hllc --with-stars=GEAR --with-feedback=none --with-grackle=$GRACKLE_ROOT

for the others:
    --with-rt=GEAR_3 --with-rt-riemann-solver=GLF --with-hydro=gizmo-mfv --with-riemann-solver=hllc --with-stars=GEAR --with-feedback=none --with-grackle=$GRACKLE_ROOT

Note that the tests which have reference solutions can't be reproduced by the
GEAR RT scheme as-is, because they require the gas density to be fixed throughout
the entire run. This can't be done for Gizmo-MFV hydrodynamics as easily as for
other SPH schemes, where fixing the particle positions suffices to keep the density
constant. If you want to fix the particle densities nonetheless, please consult the
instructions provided in 
https://github.com/SWIFTSIM/swiftsim-rt-tools/blob/main/additionalTests/instructions/GEARRT_turn_off_hydrodynamics_evolution.md


To use the SPHM1 RT model, compile with :
for propagation test:
    --with-rt=SPHM1RT_4 --with-stars=basic --with-feedback=none   --with-sundials=$SUNDIALS_ROOT

for Stromgren3D test:
    --with-rt=SPHM1RT_4 --with-stars=basic --with-feedback=none   --with-sundials=$SUNDIALS_ROOT

for Stromgren3D test without dynamics (no acceleration and no velocity):
    --with-rt=SPHM1RT_4 --with-stars=basic --with-feedback=none   --with-sundials=$SUNDIALS_ROOT --enable-boundary-particles=262145 --enable-fixed-boundary-particles=262145 

SUNDIALS_ROOT is the root directory that contains the lib and include directories, e.g. on cosma:
SUNDIALS_ROOT=/cosma/local/sundials/5.1.0/