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krome-CSE

The chemistry code KROME is in the process of being made compatible with our AGB circumstellar envelope (CSE) chemistry, usually calculated using the UMIST Rate22-CSE code, see also this link.

Aim: Couple KROME to PHANTOM to run 3D hydro-chem model of AGB outflow.

Why KROME?: KROME is implemented in such a way that it can deal with running in parallel, which is needed for a coupling with PHANTOM.

Notes

  • KROME was once coupled to PHANTOM by W. Homan, see code here. --> Didn't work as it should, chemically speaking.

  • Chemical networks were added to KROME for AGB outflows by J. Bolte, see details here.

How to run?

Clone using the recursive option: git clone --recursive, to also clone the KROME package.

  1. Run the bash script
build_UMIST.sh chem_netw

with a chemical network as argument.

  1. Run the bash script
make_CSEkrome.sh

This will make an executable for file CSE_run_krome.f.

  1. Run the bash script
run_CSE_krome.sh

with a inputfile as argument to properly run the executable.

Updates

(Latest first)

  • 12/09/'24:

    Added benchmark to results from ChemPy, see figure below.

    Discrepancy in CO between UMIST model and ChemPy model is due to CO self-shielding; this is not present in the ChemPy model.

  • 06/09/'24:

    Added test input file so that users can do a test run.

    Benchmark: Still something wrong with (probably) the density/photodissociation.

  • 06/08/'24:

    1. Found the first bug in the system!! Because of a typo (on my side), the cosmic ray reaction rates were way to high. Fixed this.

    2. In our setup, every timestep the density is lower ($\frac{1}{^2}$-law in density). Hence, we cannot use the -useN flag (using number densities), but have to use the -useX flag (fractions). This fixes a lot!

    --> Results now are getting decent :D

    To do: The photodissociation know seems to set in too late, and too few electrons. See figure, dotted lines are the abundances calculated by the UMIST Rate22-CSE code ("absolute truth"), full lines are the abundances calculated by KROME. The dashed lines are results for the same physical setup by ChemPy. First decent results

  • 31/07/'24:

    Reading in parent species file + physical input parameters works. Initialising KROME works. Saving output of KROME works.

    KROME chemical evolution does NOT coincide with our UMIST Rate22-CSE code. We (Mats Esseldeurs and me, Silke Maes) think the issue lies within the cosmic ray reaction of H2. In the UMIST Rate22-CSE code it is assumed that H2 is fully self-shielding, so that it stays roughly constant throughout the CSE. At the moment, this assumption is not yet realised in the kromeCSE code.

    Note to self: Abundances (resulting from KROME) change when using -useX (mass fractions) or -useN (number density). Check later why!

  • 12/07/'24:

    Correct rates, including radiation parameters $A_V$ and $\xi$ implemented (more info see Maes et al. 2024), via script

    umist2krome_custm.py

    originally written by Tommaso Grassi.

  • 08/07/'24:

    KROME runs, but the radiation component for the photodissociation reactions does not work yet.