In situ Analysis

Nyx supports in situ visualization using Ascent, and can leverage AMReX’s Sensei visualization pipeline. Additionally, Nyx supports in situ halo finding using Reeber2. This is useful both as in situ analysis tool, and for subgrid models, like AGN (under development).

These insitu calls are controlled by input flags, in this example analysis happens starting after step 100, for step 199, 299, and so on and so forth: = 100
insitu.start = 100

Additionally, we can request analysis at specific redshifts, and Nyx will adjust the time-stepping to reach those red-shifts exactly:

nyx.analysis_z_values = 7.0 6.0 5.0 4.0 3.0 2.0

Ascent visualization

The primary example of this functionality is in Nyx/Exec/LyA. To compile with Ascent, add in GNUmakefile.summit:


The ascent_actions.yaml file will determine while the code is running what the Ascent publish action does. The ascent_actions_slicefile.yaml file gives an example of saving slice data, rather than an image file, while the simulation is running.

To build Ascent with Conduit for other machines and configurations, see Building Ascent. For further information about using Ascent with AMReX-based applications, see AMReX Blueprint Tutorial and WarpX Ascent InSitu Documentation.

Sensei interface

See AMReX documentation: SENSEI

Halo finding

To find halos in situ while Nyx is running we use the Reeber package. To compile with Reeber, add in GNUmakefile:


and set the location of Boost library:

BOOST_INLUDE_DIR := ${BOOST_ROOT}/include/boost

GNUmake will default to:

DIY_INCLUDE_DIR ?= ../../../diy/include
REEBER_EXT_HOME ?= ../../../Reeber2

Note that these codes are in separate repositories and are not included in Nyx distribution. If you intend to use in situ halo finding, you should clone Reeber from its GitHub page and follow the installation instructions provided there.

In the Nyx inputs file, one should specify the time step interval for halo finder, fields which will be used (to use the total density, one should specify both (gas) density and particle_mass_density), and thresholds of the boundary and extrema values:

# Halo Finder
reeber.halo_int = 1
reeber.negate = 1
reeber.halo_density_vars = density particle_mass_density
reeber.halo_extrema_threshold = 20
reeber.halo_component_threshold = 10

# Call reeber insitu analysis
insitu.reeber_int = 100