External Links and Literature Page

• ​AstroBEAR — AstroBEAR's website.

Literature

Numerics

• ​Carroll-Nellenback et al. — Paper discussing implementation of AMR in AstroBEAR 2.0]
• ​AMR Defined — The ​Wikipedia entry for AMR.
• ​AMR tutorial — An overview of the Adaptive Mesh Refinement algorithm.
• ​BearCLAW Manual — ​Sorin's manual for the original ​BEARCLAW code, includes an algorithmic view of AMR.
• ​Berger & Oliger, 1984 — Dr. Berger's original AMR paper.
• ​Berger and Rigoutsos, 1991 — Outlines the Berger-Rigoutsos algorithm used to refine the AMR grids.
• ​Cunningham et al. 2007 — Sections 3 and 4 discuss the use of AMR in MHD.

Radiation Transfer

• ​Jiang et al. 2012 — A Godunov Method for Multidimensional Radiation Magnetohydrodynamics based on a variable Eddington tensor
• ​Davis et al. 2012 — A Radiation Transfer Solver for Athena using Short Characteristics

Jonathan's Super Numerical Library

• ​Sanders et al. 1998 — H viscosity method cited in Gardiner & Stone 08.
• ​Mignone 2007 — A simple and accurate Riemann solver for isothermal MHD
• ​Mignone et al. 2005 — The Piecewise Parabolic Method for Multidimensional Relativistic Fluid Dynamics
• ​Colella & Woodward 1983 — The Piecewise Parabolic Method (PPM) for gas-dynamical simulations
• ​Falle et al. 1998 — A multidimensional upwind scheme for magnetohydrodynamics
• ​Mignone et al 2007 — PLUTO: a Numerical Code for Computational Astrophysics
• ​Gardiner & Stone 2007 — An unsplit Godunov method for ideal MHD via constrained transport in three dimensions
• ​Gardiner & Stone 2004 — An unsplit Godunov method for ideal MHD via constrained transport
• ​Gardiner & Stone 2008 — Athena: A New Code for Astrophysical MHD
• ​Miyoshi & Kusano 2005 — A multi-state HLL approximate Riemann solver for ideal magnetohydrodynamics
• ​Miller & Colella 2002 — A Conservative Three-Dimensional Eulerian Method for Coupled Solid–Fluid Shock Capturing
• ​Colella and Sekora 2008 - A Limiter for PPM that Preserves Accuracy at Smooth Extrema
• ​Sekora and Colella 2009 - Extremum-Preserving Limiters for MUSCL and PPM

Alternate AMR Forms

• ​The RAMSES Code — A cell-based AMR implementation.
• ​Khokhlov, 1998 — The paper outlining the Fully-Threaded Tree algorithm used in RAMSES.
• ​Teyssier, 2002 — The first paper about the RAMSES code.

Self-Gravity / Core Collapse Papers

• ​Krumholz et al. — Sink Particle algorithm
• ​Federrath et al. — Alternative Sink Particle algorithm
• ​Truelove et al, 1997 — A 1D test of a core-collapse model.
• ​Matsumoto and Hanawa, 2003 — Lots of 2D numerical simulations of collapsing clouds.
• ​Banerjee et al, 2004 — A good starting point, containing a useful analytical model of a Bonnor-Ebert sphere.

Gravo-turbulence Papers

• Index — Comprehensive list of publications on the subject.

Planetary Nebulae Papers

• ​PN Index — Martin/Erica's index of papers.

JETSET Papers

• The original PDF may be found ​here, or as an attachment to this wiki page.
• ​Chevalier & Imamura, 1982 — Pertains to the radiative shock problem in the ​JetSet code comparison.
• ​Gaetz, Edgar & Chevalier, 1988 — More !JETSET radiative shock info.
• ​Miura & Pritchett, 1982 — Pertains to the JETSET Kelvin-Helmholtz problem.

Cooling and various microphysics

• ​Smith & Rosen, 2003 — Very nice appendix outlining various cooling and chemical processes
• ​Dalgarno & McCray, 1972 — Provides the cooling curve we use.

Other Useful Papers

• ​de Colle & Raga, 2006 — 2.5D MHD radiative YSO jets and their Halpha emission
• ​Inoue & Inutsuka, 2008 — Describes IICool method
• ​Koyoma and Inutsuka 2000 — Describes microphysics behind IICool curve
• ​Berger & Colella, 1989 — Discusses AMR in a hydrodynamic shock.
• ​Poludnenko et al. 2002 — One of our group's first AMR research papers.
• ​Miniati & Colella, 2006 — Contains useful information about working with stiff source terms.

External Links

Programming

• ​Intel Fortran Compiler — Official site for Intel's Fortran compiler.
• ​Intel's BlueGene Fortran comipler documentation
• ​Fortran tutorial — A Fortran 90 tutorial from the University of Liverpool.
• ​Subversion (aka SVN) — The open-source version control project we use.
• ​SWIG — A utility that takes C modules and generates Python wrappers for them. Useful if you want to extend VisIt's HDF5 capabilities and don't know Python very well.

Parallel Computing

• ​MPI-CH — MPI tutorial and home page for MPI-CH.
• ​MPI tutorial — MPI tutorial and API reference.
• ​OpenMPI — Official site for the OpenMPI specificaion.
• ​OpenMP — Official site for the OpenMP specification.
• ​OpenMP tutorial — A much more accessible OpenMP tutorial and reference site.

HDF5 Document Format

• ​HDF5 — Official website for HDF5 specification.
• ​Chombo HDF — Specifications for the Chombo HDF file format.

Visualization Packages

• ​ChomboVis — Official website for ChomboVis visualization package.
• ​VisIt — Official website for VisIt visualization package.
• ​PGPlot — A plotting package used within AstroBEAR.
• ​OpenDX — A visualization package supported by AstroBEAR.

Miscellaneous

• ​CFD-Wiki — The free computational fluid dynamics wiki.

Books

Programming

• ​An Introduction to Fortran 90 for Scientific Computing — by Ortega, James M. — A very short introduction to Fortran 90 programming, makes an excellent reference for simple stuff. This book is in the UR library.