bcfriesen / nyx

An adaptive mesh, N-body hydro cosmological simulation code

Nyx

an adaptive mesh, cosmological simulation code

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PLEASE NOTE: Nyx has been migrated from BoxLib to AMReX.

If you would like to use the latest version of Nyx, you will need to download AMReX from

https://github.com/AMReX-codes/amrex

Nyx is an N-body hydro cosmological simulation code with adaptive mesh refinement (AMR). Nyx uses an unsplit PPM approach for the hydrodynamics, a particle representation of dark matter, and multigrid to solve the Poisson equation for self-gravity.

Nyx is parallelized with MPI + OpenMP.

More information on Nyx can be found here:

http://amrex-astro.github.io/Nyx/

If you prefer to run with the BoxLib-based version, then you can use the "boxlib" branch (which will no longer be updated).

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Getting Started

There is a User's Guide in Nyx/UsersGuide/ (type make to build from LaTeX source) that will guide you through running your first problem.

Development Model

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). No changes should ever be pushed directly into master.

On the first workday of each month, we perform a merge of development into master, in coordination with amrex. 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 -> master is done, the merge window reopens.

Physics Included

For the description of the N-body and adiabatic hydro algorithms in Nyx, see Almgren, Bell, Lijewski, Lukic & Van Andel (2013), ApJ, 765, 39: http://adsabs.harvard.edu/abs/2013ApJ...765...39A

For the reaction and thermal rates of the primordial chemical composition gas (and convergence tests in the context of the Lyman-alpha forest), see Lukic, Stark, Nugent, White, Meiksin & Almgren (2015), MNRAS, 446, 3697: http://adsabs.harvard.edu/abs/2015MNRAS.446.3697L

For the synthesis model of the UV background, which provides the photo-ionization and photo-heating rates, we include the prescription of Onorbe, Hennawi & Lukic (2016): http://adsabs.harvard.edu/abs/2016arXiv160704218O

Post-processing

Nyx interfaces with two post-processing suites, Reeber and Gimlet. Reeber uses topological methods to construct merge trees of scalar fields, which Nyx in turn uses to find dark matter halos. Gimlet computes a variety of quantities about the simulation, including optical depths, Lyman-alpha fluxes, power spectra (both 1-D "line-of-sight" as well as fully 3-D), and probability distribution functions. These suites are fully MPI-parallel and can be run either "in situ" or "in-transit", or with a combination of both. A detailed description of their usage is provided in the Nyx User Guide.

Mailing List

For questions on how to use Nyx, email Ann Almgren at [email protected]

For more information about the science being done with Nyx, email Zarija Lukic at [email protected]

You can also subscribe to the nyx-help mailing list at google groups:

https://groups.google.com/forum/#!forum/nyx-help