zhichen3 / microphysics

common astrophysical microphysics routines with interfaces for the different AMReX codes

Microphysics

A collection of astrophysical microphysics routines for stellar explosions

There are several core types of microphysics routines hosted here:

• EOS/: these are the equations of state. All of them accept a struct called eos_t to pass the thermodynamic state information in and out, though in C++ they are templated such that they can accept other objects with members of the same name.

• integration/: this holds the various ODE integrators. VODE is the primary integrator for production use, but other integrators are provided for experimentation.

• interfaces/: this holds the structs used to interface with the EOS and networks.

• networks/: these are the reaction networks. They serve both to define the composition and its properties, as well as describe the reactions and energy release when reactions occur.

• neutrinos/: this holds the plasma neutrino cooling routines used in the reaction networks.

• rates/: this contains some common rate routines used by the various aprox networks, and could be expanded to contain other collections of rates in the future

• screening/: the screening routines for nuclear reactions. These are called by the various networks

• unit_test/: code specific to unit tests within this repo. In particular,

  • test_eos will test an equation of state by first calling it will (rho, T), and then calling it with other inputs to recover rho and/or T. A cube of data, with rho, T, and X is tested.

  • test_react will call a reaction network on a cube of data (rho, T, X).

  • test_rhs will evaluate the right-hand-side of a network without integrating it.

  • test_sdc tests integration using the set of variables for simplified SDC.

  • test_jac evaluates the Jacobian for comparison between the analytical and numerical Jacobians.

  • test_screening evaluates the screening routines.

• util: linear algebra routines for the integrators (specifically a linear system solver from LINPACK), other math routines, and build scripts

AMReX-Astro Codes

At the moment, these routines are written to be compatible with the AMReX-Astro codes, Maestro and Castro.

• Castro: http://amrex-astro.github.io/Castro/

• MAESTROeX: http://amrex-astro.github.io/MAESTROeX/

To use this repository with AMReX codes, set MICROPHYSICS_HOME to point to the Microphysics/ directory.

There are various unit tests that work with the AMReX build system to test these routines.

Other Simulation Codes

The interfaces are fairly general, so they can be expanded to other codes. This will require adding any necessary make stubs for the code's build system as well as writing unit tests for that build system to ensure the interfaces are tested.

Documentation

A user's guide for Microphysics is available at: http://amrex-astro.github.io/Microphysics/docs/

The sphinx source for the documentation is in Microphysics/sphinx_docs/

Development Model:

Development generally follows the following ideas:

• New features are committed to the development branch.

  Nightly regression testing is used to ensure that no answers change (or if they do, that the changes were expected).

  If a change is critical, we can cherry-pick the commit from development to main.

• Contributions are welcomed from anyone. Any contributions that have the potential to change answers should be done via pull requests. A pull request should be generated from your fork of Microphysics and target the development branch. (If you mistakenly target main, we can change it for you.)

  Please add a line to CHANGES summarizing your change if it is a bug fix or new feature. Reference the PR or issue as appropriate. Additionally, if your change fixes a bug (or if you find a bug but do not fix it), and there is no current issue describing the bug, please file a separate issue describing the bug, regardless of how significant the bug is. If possible, in both the CHANGES file and the issue, please cite the pull request numbers or git commit hashes where the problem was introduced and fixed, respectively.

  If there are a number of small commits making up the PR, we may wish to squash commits upon merge to have a clean history. Please ensure that your PR title and first post are descriptive, since these will be used for a squashed commit message.

• On the first workday of each month, we perform a merge of development into main, in coordination with AMReX, Maestro, and Microphysics. For this merge to take place, we need to be passing the regression tests.

  To accommodate this need, we close the merge window into development a few days before the merge day. While the merge window is closed, only bug fixes should be pushed into development. Once the merge from development -> main is done, the merge window reopens.

Core Developers

People who make a number of substantive contributions will be named "core developers" of Microphysics. The criteria for becoming a core developer are flexible, but generally involve one of the following:

• 10 non-merge commits to Microphysics/ (including Docs/) or one of the problems that is not your own science problem or

• addition of a new algorithm / module or

• substantial input into the code design process or testing

Core developers will be recognized in the following ways:

• invited to the group's slack team

• listed in the User's Guide and website as a core developer

• invited to co-author general code papers / proceedings describing Microphysics, its performance, etc. (Note: science papers will always be left to the science leads to determine authorship).

If a core developer is inactive for 3 years, we may reassess their status as a core developer.

Getting help

We use github discussions for requesting help and interacting with the community:

https://github.com/amrex-astro/Microphysics/discussions