An adaptive mesh, N-body hydro cosmological simulation code
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README.md

Nyx

an adaptive mesh, massively-parallel, cosmological simulation code


About

Nyx code solves equations of compressible hydrodynamics on an adaptive grid hierarchy coupled with an N-body treatment of dark matter. The gasdynamics in Nyx uses a finite volume methodology on an adaptive set of 3-D Eulerian grids; dark matter is represented as discrete particles moving under the influence of gravity. Particles are evolved via a particle-mesh method, using Cloud-in-Cell deposition/interpolation scheme. Both baryonic and dark matter contribute to the gravitational field. In addition, Nyx currently includes physics needed to accurately model the intergalactic medium: in optically thin limit and assuming ionization equilibrium, the code calculates heating and cooling processes of the primordial-composition gas in an ionizing ultraviolet background radiation field. Additional physics capabilities are under development.

Nyx is parallelized with MPI + OpenMP, and has been run at parallel concurrency of up to 2,097,152 (on NERSC's Cori).

More information on Nyx can be found here: http://amrex-astro.github.io/Nyx/

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

Getting Started

To compile the code, we require Fortran 2003 and C++11 compliant compilers that support (if parallelism is sought) OpenMP 4.5 or better, and/or MPI-2 or higher implementation.

To use Nyx, you also need AMReX: https://github.com/AMReX-codes/amrex

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. We use nightly regression testing to ensure that no answers change (or if they do, that the changes were expected). No changes should be pushed directly into master. Approximately once a month, we perform a merge of development into master.

Contributions are welcomed and should be done via pull requests. A pull request should be generated from your fork of Nyx and should target the development branch.

Physics

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 considerations regarding the spatially uniform synthesis model of the UV background, which provides the photo-ionization and photo-heating rates, see Onorbe, Hennawi & Lukic (2017), ApJ, 837, 106: http://adsabs.harvard.edu/abs/2017ApJ...837..106O

We have also implemented non-radiative transfer methods to model inhomogeneous reionization, the paper is in preparation.

Output

Nyx outputs certain global diagnostics at each timestep and plot files at regular intervals, or at user-specified redshifts. Visualization packages VisIt, Paraview and yt have built-in support for the AMReX file format used by Nyx.

In addition, 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 halos. Gimlet computes a variety of quantities related to the Lyman-alpha forest science. These suites are fully MPI-parallel and can be run either "in situ" or "in-transit", or with a combination of both.

License

Nyx is released under the LBL's modified BSD license, see the license.txt file for details.

Contact

For questions, comments, suggestions, contact Ann Almgren at ASAlmgren@lbl.gov or Zarija Lukic at zarija@lbl.gov .