Samuel W. Skillman

YT: A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/) an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzos structure adaptive mesh refinement data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation, and topologically connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.

ENZO: AN ADAPTIVE MESH REFINEMENT CODE FOR ASTROPHYSICS

This paper describes the open-source code Enzo, which uses block-structured adaptive mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in one, two, and three dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the codes parallel performance, and discuss the Enzo collaborations code development methodology.

Cosmological Shocks in Adaptive Mesh Refinement Simulations and the Acceleration of Cosmic Rays

We present new results characterizing cosmological shocks within adaptive mesh refinement N-body/hydrodynamic simulations that are used to predict nonthermal components of large-scale structure. This represents the first study of shocks using adaptive mesh refinement. We propose a modified algorithm for finding shocks from those used on unigrid simulations that reduces the shock frequency of low Mach number shocks by a factor of ~3. We then apply our new technique to a large, (512 h−1 Mpc)3, cosmological volume and study the shock Mach number () distribution as a function of preshock temperature, density, and redshift. Because of the large volume of the simulation, we have superb statistics that result from having thousands of galaxy clusters. We find that the Mach number evolution can be interpreted as a method to visualize large-scale structure formation. Shocks with 20 generally follow accretion onto filaments and galaxy clusters, respectively. By applying results from nonlinear diffusive shock acceleration models using the first-order Fermi process, we calculate the amount of kinetic energy that is converted into cosmic-ray protons. The acceleration of cosmic-ray protons is large enough that in order to use galaxy clusters as cosmological probes, the dynamic response of the gas to the cosmic rays must be included in future numerical simulations.

COSMOLOGICAL MAGNETOHYDRODYNAMIC SIMULATIONS OF GALAXY CLUSTER RADIO RELICS: INSIGHTS AND WARNINGS FOR OBSERVATIONS

Non-thermal radio emission from cosmic-ray electrons in the vicinity of merging galaxy clusters is an important tracer of cluster merger activity, and is the result of complex physical processes that involve magnetic fields, particle acceleration, gas dynamics, and radiation. In particular, objects known as radio relics are thought to be the result of shock-accelerated electrons that, when embedded in a magnetic field, emit synchrotron radiation in the radio wavelengths. In order to properly model this emission, we utilize the adaptive mesh refinement simulation of the magnetohydrodynamic evolution of a galaxy cluster from cosmological initial conditions. We locate shock fronts and apply models of cosmic-ray electron acceleration that are then input into radio emission models. We have determined the thermodynamic properties of this radio-emitting plasma and constructed synthetic radio observations to compare observed galaxy clusters. We find a significant dependence of the observed morphology and radio relic properties on the viewing angle of the cluster, raising concerns regarding the interpretation of observed radio features in clusters. We also find that a given shock should not be characterized by a single Mach number. We find that the bulk of the radio emission comes from gas with T > 5 ? 107 K, ? ~ 10?28-10?27 g cm?3, with magnetic field strengths of 0.1-1.0 ?G, and shock Mach numbers of . We present an analysis of the radio spectral index which suggests that the spatial variation of the spectral index can mimic synchrotron aging. Finally, we examine the polarization fraction and position angle of the simulated radio features, and compare to observations.

GALAXY CLUSTER RADIO RELICS IN ADAPTIVE MESH REFINEMENT COSMOLOGICAL SIMULATIONS: RELIC PROPERTIES AND SCALING RELATIONSHIPS

Cosmological shocks are a critical part of large-scale structure formation, and are responsible for heating the intracluster medium in galaxy clusters. In addition, they are capable of accelerating non-thermal electrons and protons. In this work, we focus on the acceleration of electrons at shock fronts, which is thought to be responsible for radio relics—extended radio features in the vicinity of merging galaxy clusters. By combining high-resolution adaptive mesh refinement/N-body cosmological simulations with an accurate shock-finding algorithm and a model for electron acceleration, we calculate the expected synchrotron emission resulting from cosmological structure formation. We produce synthetic radio maps of a large sample of galaxy clusters and present luminosity functions and scaling relationships. With upcoming long-wavelength radio telescopes, we expect to see an abundance of radio emission associated with merger shocks in the intracluster medium. By producing observationally motivated statistics, we provide predictions that can be compared with observations to further improve our understanding of magnetic fields and electron shock acceleration.

THE CONCENTRATION DEPENDENCE OF THE GALAXY–HALO CONNECTION: MODELING ASSEMBLY BIAS WITH ABUNDANCE MATCHING

Empirical methods for connecting galaxies to their dark matter halos have become essential in interpreting measurements of the spatial statistics of galaxies. Among the most successful of these methods is the technique of subhalo abundance matching, which has to date been used to associate galaxy properties with a small set of halo properties. We generalize this set of halo properties to allow variable dependence on halo concentration, and parameterize the degree of concentration dependence with a single parameter. This parameter provides a smooth interpolation between abundance matching to peak halo mass and to peak halo circular velocity. We characterize the influence of this parameter on two-point clustering, the satellite fraction, and the degree of galaxy assembly bias. We also evaluate the degeneracies between the concentration dependence and the scatter in the abundance matching relation. We show that low redshift clustering measurements from SDSS prefer a moderate amount of concentration dependence --- more than would be indicated by matching galaxy luminosity to the peak halo mass, and less than would be indicated by matching to the peak halo circular velocity. We also show that these results are robust to moderate changes in cosmological parameters, and that the best-fit model from two-point clustering agrees with previous measurements of the satellite fraction. We note that statistical constraints on these models have been (and still are, in most regimes) limited primarily by sample variance in the limited-size simulations, and not in the data. We discuss physical interpretations of these results and their implications for the galaxy-halo connection.

HOW WELL DO COSMOLOGICAL SIMULATIONS REPRODUCE INDIVIDUAL HALO PROPERTIES

Cosmological simulations of galaxy formation often rely on prescriptions for star formation and feedback that depend on halo properties such as halo mass, central overdensity, and virial temperature. In this paper, we address the convergence of individual halo properties, based on their number of particles N, focusing, in particular, on the mass of halos near the resolution limit of a simulation. While it has been established that the halo mass function is sampled on average down to N ~ 20-30 particles, we show that individual halo properties exhibit significant scatter, and some systematic biases, as one approaches the resolution limit. We carry out a series of cosmological simulations using the Gadget2 and Enzo codes with Np = 643 to Np = 10243 total particles, keeping the same large-scale structure in the simulation box. We consider boxes of small (l box = 8 Mpc h –1), medium (l box = 64 Mpc h –1), and large (l box = 512 Mpc h –1) size to probe different halo masses and formation redshifts. We cross-identify dark matter halos in boxes at different resolutions and measure the scatter in their properties. The uncertainty in the mass of single halos depends on the number of particles (scaling approximately as N –1/3), but the rarer the density peak, the more robust its identification. The virial radius of halos is very stable and can be measured without bias for halos with N 30. In contrast, the average density within a sphere containing 25% of the total halo mass is severely underestimated (by more than a factor 2) and the halo spin is moderately overestimated for N 100. If sub-grid physics is implemented upon a cosmological simulation, we recommend that rare halos (~3σ peaks) be resolved with N 100 particles and common halos (~1σ peaks) with N 400 particles to avoid excessive numerical noise and possible systematic biases in the results.

On the Road to More Realistic Galaxy Cluster Simulations: The Effects of Radiative Cooling and Thermal Feedback Prescriptions on the Observational Properties of Simulated Galaxy Clusters

Flux-limited X-ray surveys of galaxy clusters show that clusters come in two roughly equally proportioned varieties: cool core clusters (CCs) and non-cool core clusters (NCCs). In previous work, we have demonstrated using cosmological N-body + Eulerian hydrodynamic simulations that NCCs are often consistent with early major merger events that destroy embryonic CCs. In this paper we extend those results and conduct a series of simulations using different methods of gas cooling and of energy and metal feedback from supernovae, where we attempt to produce a population of clusters with realistic central cooling times, entropies, and temperatures. We find that the use of metallicity-dependent gas cooling is essential to prevent early overcooling, and that adjusting the amount of energy and metal feedback can have a significant impact on observable X-ray quantities of the gas. We are able to produce clusters with more realistic central observable quantities than have previously been attained. However, there are still significant discrepancies between the simulated clusters and observations, which indicates that a different approach to simulating galaxies in clusters is needed. We conclude by looking toward a promising subgrid method of modeling galaxy feedback in clusters that may help to ameliorate the discrepancies between simulations and observations.

COSMOLOGICAL SIMULATIONS OF ISOTROPIC CONDUCTION IN GALAXY CLUSTERS

Simulations of galaxy clusters have a difficult time reproducing the radial gas-property gradients and red central galaxies observed to exist in the cores of galaxy clusters. Thermal conduction has been suggested as a mechanism that can help bring simulations of cluster cores into better alignment with observations by stabilizing the feedback processes that regulate gas cooling, but this idea has not yet been well tested with cosmological numerical simulations. Here we present cosmological simulations of 10 galaxy clusters performed with five different levels of isotropic Spitzer conduction, which alters both the cores and outskirts of clusters, though not dramatically. In the cores, conduction flattens central temperature gradients, making them nearly isothermal and slightly lowering the central density, but failing to prevent a cooling catastrophe there. Conduction has little effect on temperature gradients outside of cluster cores because outward conductive heat flow tends to inflate the outer parts of the intracluster medium (ICM), instead of raising its temperature. In general, conduction tends reduce temperature inhomogeneity in the ICM, but our simulations indicate that those homogenizing effects would be extremely difficult to observe in ~5?keV clusters. Outside the virial radius, our conduction implementation lowers the gas densities and temperatures because it reduces the Mach numbers of accretion shocks. We conclude that, despite the numerous small ways in which conduction alters the structure of galaxy clusters, none of these effects are significant enough to make the efficiency of conduction easily measurable, unless its effects are more pronounced in clusters hotter than those we have simulated.

THE PROPERTIES OF X-RAY COLD FRONTS IN A STATISTICAL SAMPLE OF SIMULATED GALAXY CLUSTERS

We examine the incidence of cold fronts in a large sample of galaxy clusters extracted from a (512 h –1 Mpc) hydrodynamic/N-body cosmological simulation with adiabatic gas physics computed with the Enzo adaptive mesh refinement code. This simulation contains a sample of roughly 4000 galaxy clusters with M ≥1014 M ☉ at z = 0. For each simulated galaxy cluster, we have created mock 0.3-8.0 keV X-ray observations and spectroscopic-like temperature maps. We have searched these maps with a new automated algorithm to identify the presence of cold fronts in projection. Using a threshold of a minimum of 10 cold front pixels in our images, corresponding to a total comoving length L cf>156 h –1 kpc, we find that roughly 10%-12% of all projections in a mass-limited sample would be classified as cold front clusters. Interestingly, the fraction of clusters with extended cold front features in our synthetic maps of a mass-limited sample trends only weakly with redshift out to z = 1.0. However, when using different selection functions, including a simulated flux limit, the trending with redshift changes significantly. The likelihood of finding cold fronts in the simulated clusters in our sample is a strong function of cluster mass. In clusters with M>7.5 × 1014 M ☉ the cold front fraction is 40%-50%. We also show that the presence of cold fronts is strongly correlated with disturbed morphology as measured by quantitative structure measures. Finally, we find that the incidence of cold fronts in the simulated cluster images is strongly dependent on baryonic physics.