Python tools for HARM analysis. Full documentation is here.
pyharm is a library of Python functions and scripts for analyzing and plotting the output of General-Relativistic Magnetohydrodynamic (GRMHD) simulations. It includes functions for obtaining a long list of different variables of interest (pressures, temperatures, stress-energy tensor, synchrotron emissivity) based on local fluid state. It additionally includes reductions for performing surface and volume integrals of various types, sophisticated plotting tools, and MPI-accelerated scripts for quickly and efficiently producing movies and time-summed or -averaged reductions over large-scale simulations.
pyharm primarily supports simulations based on the HARM scheme (Gammie et al. 2003) -- KHARMA, iharm3d, and ebhlight. It includes Python re-implementations of core parts of the scheme, useful for deriving everything about the simulation not directly present in output files. It includes limited support for several other codes, either directly or after translation with EHT-babel.
The core of pyharm is the FluidState object, which behaves similar to a Python dictionary of numpy arrays, but calculates its members on the fly by reading the original file and performing operations only as necessary ("lazy" evaluation). FluidState objects can be sliced similarly to numpy arrays, and subsequent file reads and calculations will be done over only the sliced portion. Between lazy evaluation and heavy parallelization through multiprocessing and MPI, pyharm is fast and scalable -- the default scripts are able to process TB of simulation output per minute.
As a consequence of needing to read GRMHD output, pyharm includes definitions of various coordinate systems in Kerr spacetime, as well as tools for dealing with a evenly spaced logically Cartesian grids under many different coordinate systems and transformations. These might be independently useful, see coordinates.py & grid.py if you're looking for just coordinate tools.
The preferred installation method is to run simply:
$ pip3 install -e .Thereafter pyharm should be importable from any Python prompt or script run in the same environment. This command installs pyharm as "editable," so that changes to the source will be reflected immediately when next importing the package -- this is recommended, as it is expected that users will have to modify the source code eventually. pyharm can also be installed as a user or system package, but at the cost of less easily modifying the source.
If you're skeptical of using a big library just to read HDF5 files, the notebooks directory has a sample Jupyter notebook playing around with some of the things that make pyharm cool & potentially useful to you. The full developer reference is here. Or for the dev branch, here.
If you're more interested in ready-made tools, try calling pyharm-movie for producing plots and movies, and pyharm-analysis for performing reductions over a full simulation's output. These and the other pyharm scripts are added to your $PATH upon installation, so they're always available. There are quite a few different movies and analyses implemented, and new ones can be added easily by adding to pyharm.plots.figures to extend pyharm-movie, or pyharm.ana.analyses to extend pyharm-analysis. New additions to those files will automatically become valid arugments to pyharm-movie and pyharm-analysis, show up as options in the help, etc.
Several parts of pyharm try to parse strings to determine behavior, to specify a desired variable, plot, or result from the command line or quickly in notebooks. These replace what might traditionally be member functions of e.g. the FluidState object (think dump.ucov()) with what acts like a giant Python dictionary (dump['ucov']). Each "item" is computed at first access and cached thereafter.
Since it's possible to combine keys in arbitrary ways, there is no master list of valid keys, nor does it make sense to write e.g. for key in dump or if "key" in dump. The most reliable way to determine whether something can be computed is to try it, and catch the ValueError (for unknown keys) or IOError (for known keys not present in a file) if it is not found.
That said, a good starter list, with references to more complete lists, can be found in the documentation.