# Analyzing Outputs¶

For analysis and visualizations purposes, Nyx outputs plotfiles with user-defined grid quantities and/or particle data. This file format is native to the AMReX framework, but there is also an option to use HDF5 outputs (this is implemented and is in a testing/optimization phase now).

## Visualization¶

There are several visualization tools that can be used for AMReX plotfiles, specifically VisIt, ParaView, and yt.

See the AMReX documentation for guidance on how to use each of these tools.

The following inputs control when plotfiles are written

Description Type Default
amr.plot_int Frequency of plotfile output; if -1 then no plotfiles will be written Int -1
amr.plotfile_on_restart Should we write a plotfile when we restart (only used if plot_int>0) Bool False
amr.plot_file Prefix to use for plotfile output String plt

and the following control which variables appear in the plotfile

Description Type Default
amr.plot_vars Name of state variables to be in plotfiles Strings All
amr.plot_dervive_plot_vars Name of derived variables to be in plotfiles Strings All

Nyx also easily interfaces with two post-processing suites, Reeber used for halo finding and Gimlet, used for calculating different summary statistics.

## Reeber¶

Reeber uses topological methods to construct merge trees of scalar fields. These trees are effectively parameter-independent and contain a complete description of the field topology. In the context of Nyx, the field of interest is usually the total matter density. Nyx then queries the merge tree with user-defined runtime parameters in order to locate the volume-averaged center of dark matter halos. The same tree can be queried with any number of such parameters to find halos with different mass/density thresholds. Reeber is publicly available on GitHub.

## Gimlet¶

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. Gimlet code is not yet publicly available, but we are working on releasing it.

## Do It Yourself¶

Nyx and AMReX provide the capability for the user to execute an arbitrary post-processing workflow. In Util/Diagnostics/ we provide a simple example of opening an AMReX plotfile, reading and manipulating data in it. That can be a starting place for building analysis tools for any specific need.