Microphysics Overview

Getting Started (Standalone)

Microphysics can be used in a “standalone” fashion to run the unit tests and explore the behavior of the reaction networks. The main requirement is a copy of AMReX:

git clone https://github.com/AMReX-Codes/amrex.git

We use this for some data structures and the build system. You need to set the AMREX_HOME environment variable to point to the amrex/ directory:

export AMREX_HOME=/path/to/amrex

(where you change /path/to/amrex to your actual path).

A good unit test to start with is burn_cell – this is simply a one-zone burn. In Microphysics/ do:

cd unit_test/burn_cell
make

This will create an executable called main3d.gnu.ex. Then you can run it as:

./main3d.gnu.ex inputs_aprox21

By default, the test is built with the 21-isotope aprox21 network. Here inputs_aprox21 is the inputs file that sets options.

Getting Started (Running with MAESTROeX or CASTRO)

Getting started with Microphysics using either CASTRO or MAESTROeX is straightforward. Because the modules here are already in a format that the AMReX codes understand, you only need to provide to the code calling these routines their location on your system. The code will do the rest. To do so, define the MICROPHYSICS_HOME environment variable, either at a command line or (if you use the bash shell) through your ~/.bashrc, e.g.:

export MICROPHYSICS_HOME=/path/to/Microphysics

For CASTRO and MAESTROeX the name of the EOS and network are set via the make variables EOS_DIR and NETWORK_DIR. These codes then rely on the Microphysics Make.Microphysics_extern makefile stub (found via the MICROPHYSICS_HOME variable) to add the necessary source to the build. All of the interfaces that these codes use are found in Microphysics/interfaces/.

Other codes can use Microphysics in the same fashion. Unit tests in Microphysics/unit_test/ provide some examples of using the interfaces.

Structure

The high-level directory structure delineates the types of microphysics and the generic solvers:

  • conductivity: thermal conductivity routines

  • constants: fundamental constants

  • EOS/: the various equations of state

  • integration/: the ODE integration routines used for the reaction networks

  • interfaces/: the main structs / derived types that are used to interface with the EOS and reaction networks.

  • networks/: the nuclear reaction networks. This is mostly just the righthand side of the network, as the actual integrators are decoupled from the network.

  • neutrinos/: neutino loss source terms for the network energy equation.

  • opacity/: opacity routines for radiation transport

  • rates/: common nuclear reaction rate modules used by some of the networks.

  • screening/: common electron screening factors used by some of the reaction networks.

  • sphinx_docs: the sphinx source for this documentation

  • unit_test/: self-contained unit tests for Microphysics. These don’t need any application code to build, but will require AMReX.

  • util/: linear algebra solvers and other routines.

Design Philosophy

Any application that uses Microphysics will at minimum need to choose an EOS and a network. These two components work together. The design philosophy is that the EOS depends on the network, but not the other way around. The decision was made for the network to act as the core module, and lots of code depends on it. This avoids circular dependencies by having the main EOS datatype, eos_t, and the main reaction network datatype, burn_t, be built on top of the network.

The network is meant to store the properties of the species (typically nuclear isotopes) including their atomic weights and numbers, and also describes any links between the species when burning.

The equation of state relates the thermodynamic properties of the material. It depends on the composition of the material, typically specified via mass fractions of the species, and uses the properties of the species defined by the network to interpret the state.

We try to maximize code reuse in the Microphysics source, so the solvers (ODE integration for the network and Newton-Raphson root finding for the EOS) is separated from the specific implementations of the microphysics.

Note

All quantities are assumed to be in CGS units, unless otherwise specified.