How to plot the Mass accretion, magnetic flux and MAD parameters, with respect to time?

[mraianeto]

I've worked with three versions of HARM: harmpi, iharm3d, and iharm2d_v4, but I could not find examples in documentation folders or literature that would help me on how to plot accretion rate, magnetic flux and energy output

I also read the pyharm documentation, but it did not help. In fact using the example given in here I've plot the Mdot graph with respect to r, from a particular dump, but more than that I can't figure out. It is very odd that people didn't share direct procedures for this, since they are very important plots.

So, can you shed some light on how to plot the mass accretion, magnetic flux, and the energy output in harm3d?

[c-prather]

If you're looking for just example code, script/analysis/eht_analysis.py in this repository tries to calculate what you want, among other basic statistics. I have no idea if it still works though. If it's broken by package updates or neglect, we should clean out the script/analysis folder (which is actually an extremely old version of pyharm from before it was called pyharm) and redirect people to the newer code.

If you're looking to do science, though, I'd recommend pyharm analysis.

There's not a good tutorial for it because most pyharm users have generally been migrating from things they'd written themselves, and thus already had particular needs for how they calculated the fluxes: at the event horizon or at 5M radius? Over the disk or the whole 4pi? Should the normalized magnetization be calculated against the current accretion rate as in your example plot, a moving average as is more common now, or a global average accretion rate for the whole run? pyharm doesn't choose these defaults in the python interface, mostly because everyone coming in had their own way of doing things.

pyharm analysis represents my take on all of those decisions, and I'm not sure how many other people even use it. It is documented with pyharm analysis --help, but the gist is that pyharm analysis basic path/to/folder should spit out an HDF5 file with at least the 1D arrays /coords/t recording dump times, /t/Mdot with accretion rate, and /t/Phi_b with magnetization. These latter two are calculated at zone 5 from the inner edge, which generally corresponds to the EH, but is iirc modifiable with a command line parameter. In any case the code is here if you need to customize. The other analyses record most of the other things you would want for plotting what you see in e.g. the EHT Code Comparison. r_profiles, for example, will give you the radial profiles of mass and energy flux over time, so you can plot the time-dependent accretion rate wherever you like.

Generally, even pyharm analysis users plot this HDF5 file themselves so they can customize. pyharm does have some very limited facilities for automatically plotting it (including e.g., calculating the normalized magnetization against a moving average of accretion rate), but these are unfinished and not well documented, as I think I may have been the only heavy user. The source code in pyharm/ana_results.py is probably your best starting point for using that code, if you'd prefer not to write it yourself.

Finally, if you're just looking for the definitions, EHT's comparison has the common, coordinate-independent expressions for computing each flux.

P.S. if you're looking to do much customization or new science with the GRMHD runs, consider KHARMA which is more actively maintained than these old C codes.

I managed to use the eht_plot.py after all! Thank you!