## How to Download Nyx

You can find the latest version of the **Nyx** repository at
https://github.com/BoxLib-Codes/Nyx

The **Nyx Users' Guide** is available here.

## Nyx Email Support List

If you are interested in using Nyx, please join our Nyx mailing list to receive any updates and see questions other users are asking: https://groups.google.com/forum/#!forum/nyx-help.

## Nyx Code Papers

For the first paper describing the N-body, adiabatic hydro and gravity algorithms:

A. S. Almgren, J. B. Bell, M.J. Lijewski, Z. Lukic, E. Van Andel,
**"Nyx: A Massively Parallel AMR Code for Computational Cosmology"**
*Astrophysical Journal*, **765**, 39, 2013.
[pdf]

For the reaction and thermal rates of the primordial chemical composition gas (and convergence tests in the context of the Lyman-alpha forest), see:

Zarija Lukic, Casey Stark, Peter Nugent, Martin White, Avery Meiksin, Ann Almgren,
**"The Lyman-alpha forest in optically-thin hydrodynamical simulations,"**
*Monthly Notices of the Royal Astronomical Society*,
**446**, 3697-3724, 2015
[arxiv].

For the synthesis model of the UV background, which provides the photo-ionization and photo-heating rates, see:

Jose Onorbe, Joseph F Hennawi, Zarija Lukic,
**"Self-Consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations,"**
*submitted for publication*,
[arxiv].

## Nyx-related Papers

Daniele Sorini, Jose Onorbe, Zarija Lukic, Joseph F Hennawi,
**"Modelign the Lyman-alpha Forest in Collisionless Simulations,"**
*submitted for publication*,
[arxiv].

Brian Friesen, Ann Almgren, Zarija Lukic, Gunther Weber, Dmitriy Morozov, Vincent Beckner, Marcus Day,
**"A framework for in situ and in-transit analysis of cosmological simulations,"**,
*to appear*, 2016.

W. Schmidt, J.F. Engels, J.C. Niemeyer, A.S. Almgren,
**"Hot and Turbulent Gas in Clusters",**
*Monthly Notices of the Royal Astronomical Society*,
**459(1)**, 701-719, 2016
[arxiv].

H. Braun, W. Schmidt, J.C. Niemeyer, A.S. Almgren,
**"Large-eddy simulations of isolated disk galaxies with thermal and turbulent feedback,"**
*Monthly Notices of the Royal Astronomical Society*, **442(4)**, pp. 3407-3426, 2014.
[arxiv]

W. Schmidt, A.S. Almgren, H. Braun, J.F. Engels, J.C. Niemeyer, R.R. Mekuria, A.J. Aspden, J.B. Bell,
**"Cosmological Fluid Mechanics with Adaptively Refined Large Eddy Simulations,"**
*Monthly Notices of the Royal Astronomical Society*, **440**, pp. 3051-3077, 2014.
[arxiv]

W. Schmidt, J. Schulz, L. Iapichino, A.S. Almgren,
**" Influence of adaptive mesh refinement and the hydro solver
on shear-induced mass stripping in a minor merger scenario,"**
*Astronomy and Computing*, **9**, 49-64, March 2015
[arxiv].

## Overview

The development of Nyx began as part of an LDRD-funded project, and is continuing under funding from the SciDAC-3 project,**Computation-Driven Discovery for the Dark Universe.**Nyx is used for large-scale cosmological simulations on massively parallel machines.

## Software Framework

The Nyx software is based on the BoxLib software framework developed by CCSE.## Hydrodynamics

The hydrodynamic component of Nyx is mesh-based. Time integration of the hydro equations on the mesh is based on an unsplit version of the the piecewise parabolic method (PPM) with new limiters that avoid reducing the accuracy of the scheme at smooth extrema.## Equation of State

Nyx can follow an arbitrary number of isotopes or elements. The atomic weights and amounts of these elements are used to calculate the mean molecular weight of the gas required by the equation of state.

## Dark Matter

Dark matter is represented as particles in Nyx. Each particle has a position, a mass, and a velocity associated with it. These particles contribute their mass to the mesh for the gravity solve, and their velocities are updated by the gravitational field interpolated from the mesh.## Self-gravity

Nyx uses a full Poisson solve on the mesh for the gravitational potential due to self-gravity (from both dark matter and baryons) in cosmological simulations. The equation is discretized using standard a 7-point stencil and the resulting problem is solved using multigrid with V-cycles and Gauss-Seidel relaxation.

## AMR in Nyx

Our approach to adaptive refinement in Nyx uses a nested hierarchy of logically-rectangular grids with simultaneous refinement of the grids in both space and time. The integration algorithm on the grid hierarchy is a recursive procedure in which coarse grids are advanced in time, fine grids are advanced multiple steps to reach the same time as the coarse grids and the data at different levels are then synchronized. During the regridding step, increasingly finer grids are recursively embedded in coarse grids until the solution is sufficiently resolved. An error estimation procedure based on user-specified criteria evaluates where additional refinement is needed and grid generation procedures dynamically create or remove rectangular fine grid patches as resolution requirements change.

## Visualization

The BoxLib output file format is compatible with## Questions?

Contact Ann Almgren.## Acknowledgements

The development of Nyx began as part of an LDRD-funded project, and is continuing under funding from the SciDAC-3 project,
**Computation-Driven Discovery for the Dark Universe.**