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The AstroBEAR source code is organized into several subdirectories that each contain modules designed to handle a particular aspect of the code. Here is a very brief description of each directory.

- tree - Contains modules that define the AMR tree structures as well as various routines for manipulating the AMR tree.
- data - Contains modules that define the data structures associated with each grid or patch as well as operations for synchronizing the data, and for performing operations on the data.
- particle - Contains modules that define the data structures associated with Lagrangian particles, and routines for performing operations on particles.
- amr - Contains control routines for advancing the AMR dataset in time.
- distribution - Contains routines for distributing workloads over multiple processors.
- communication - Contains routines for performing communication needed to synchronize data across processors.
- hyperbolic - Contains routines for performing conservative hyperbolic advances.
- elliptic - Contains routines for solving linear systems of equations such as poisson's equation used by the self-gravity module.
- explicit - Contains routines for solving parabolic equations through explicit sub-cycling
- physics - Contains definitions and functions related to the particular equations being solved.
- io - Contains routines for writing and reading simulation data to disk.
- modules - Contains various routines for controlling initial and boundary conditions
- source - Contains various routines for applying source terms.
- processing - Contains routines for analyzing the data and producing various data products.
- layouts - Contains modules for mapping AMR datasets onto uniform subgrids.
- threads - Contains modules for handling threading of level advances.

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