arXiv subjects

Matthew J. Turk

Publications and source records attributed to Matthew J. Turk.

At least 19 recordsLinked to original sources

arXiv2026

libyt: an In Situ Interface Connecting Simulations with yt, Python, and Jupyter Workflows

In the exascale computing era, handling and analyzing massive datasets have become extremely challenging. In situ analysis, which processes data during simulation runtime and bypasses costly intermediate disk input and output steps, offers a promising solution. We present libyt (https://github.com/yt-project/libyt), an open-source C library that enables astrophysical simulations to analyze and visualize data in parallel computation with yt or other Python packages. libyt can invoke Python routines automatically or provide interactive entry points via a Python prompt or a Jupyter Notebook. It requires minimal intervention in researchers' workflow, allowing users to reuse job submission scripts and Python routines. We describe libyt's architecture for parallel computing in high-performance computing environments, including its bidirectional connection between simulation codes and Python, and its integration into the Jupyter ecosystem. We detail its methods for reading patch-based adaptive mesh refinement (AMR) simulations and handling in-memory data with minimal overhead, and procedures for yielding data when requested by Python. We describe how libyt maps simulation data to yt frontends, allowing post-processing scripts to be converted into in situ analysis with just two lines of change. We document libyt's API and demonstrate its integration into two astrophysical simulation codes, GAMER and Enzo, using examples including core-collapse supernovae, isolated dwarf galaxies, fuzzy dark matter, the Sod shock tube test, Kelvin-Helmholtz instability, and the AGORA galaxy simulation. Finally, we discuss libyt's performance, limitations related to data redistribution, extensibility, architecture, and comparisons with traditional post-processing approaches.

astro-ph.IM↗

arXiv2024

Why does the Milky Way have a metallicity floor?

The prevalence of light element enhancement in the most metal-poor stars is potentially an indication that the Milky Way has a metallicity floor for star formation around $\sim$10$^{-3.5}$ Z$_{\odot}$. We propose that this metallicity floor has its origins in metal-enriched star formation in the minihalos present during the Galaxy's initial formation. To arrive at this conclusion, we analyze a cosmological radiation hydrodynamics simulation that follows the concurrent evolution of multiple Population III star-forming minihalos. The main driver for the central gas within minihalos is the steady increase in hydrostatic pressure as the halos grow. We incorporate this insight into a hybrid one-zone model that switches between pressure-confined and modified free-fall modes to evolve the gas density with time according to the ratio of the free-fall and sound-crossing timescales. This model is able to accurately reproduce the density and chemo-thermal evolution of the gas in each of the simulated minihalos up to the point of runaway collapse. We then use this model to investigate how the gas responds to the absence of H$_{2}$. Without metals, the central gas becomes increasingly stable against collapse as it grows to the atomic cooling limit. When metals are present in the halo at a level of $\sim$10$^{-3.7}$ Z$_{\odot}$, however, the gas is able to achieve gravitational instability while still in the minihalo regime. Thus, we conclude that the Galaxy's metallicity floor is set by the balance within minihalos of gas-phase metal cooling and the radiation background associated with its early formation environment.

astro-ph.GA↗

arXiv2023

The Role of Radiation and Halo Mergers in Pop III Star Formation

We present a study of the co-evolution of a population of primordial star-forming minihalos at Cosmic Dawn. In this study, we highlight the influence of individual Population III stars on the ability of nearby minihalos to form sufficient molecular hydrogen to undergo star formation. In the absence of radiation, we find the minimum halo mass required to bring about collapse to be ~10^5 Msun, this increases to ~10^6 Msun after two stars have formed. We find an inverse relationship between halo mass and the time required for it to recover its molecular gas after being disrupted by radiation from a nearby star. We also take advantage of the extremely high resolution to investigate the effects of major and minor mergers on the gas content of star-forming minihalos. Contrary to previous claims of fallback of supernova ejecta, we find minihalos evacuated after hosting Pop III stars primarily recover gas through mergers with undisturbed halos. We identify an intriguing type of major merger between recently evacuated halos and gas-rich ones, finding that these 'mixed' mergers accelerate star formation instead of suppressing it like their low redshift counterparts. We attribute this to the gas-poor nature of one of the merging halos resulting in no significant rise in temperature or turbulence and instead inducing a rapid increase in central density and hydrostatic pressure. This constitutes a novel formation pathway for Pop III stars and establishes major mergers as potentially the primary source of gas, thus redefining the role of major mergers at this epoch.

astro-ph.GA↗

arXiv2020

Powderday: Dust Radiative Transfer for Galaxy Simulations

We present Powderday, a flexible, fast, open-source dust radiative transfer package designed to interface with galaxy formation simulations. Powderday builds on FSPS population synthesis models, Hyperion dust radiative transfer, and employs yt to interface between different software packages. We include our stellar population synthesis modeling on the fly, which allows for significant run-time flexibility in the assumed stellar physics. We include a model for nebular line emission that can employ either precomputed Cloudy lookup tables (for efficiency), or direct photoionization calculations for all young stars (for flexibility). The dust content follows either observationally-motivated prescriptions, direct modeling from galaxy formation simulations, or a novel approach that includes the dust content via learning-based algorithms from the SIMBA cosmological galaxy formation simulation. AGN can additionally be included via a range of prescriptions. The output of these models are broadband SEDs, as well as filter-convolved images. Powderday is designed to eliminate last-mile efforts by researchers that employ different hydrodynamic galaxy formation models, and seamlessly interfaces with GIZMO, AREPO, GASOLINE, CHANGA, and ENZO. We demonstrate the capabilities of the code via three applications: a model for the star formation rate (SFR) - infrared luminosity relation in galaxies (including the impact of AGN); the impact of circumstellar dust around AGB stars on the mid-infrared emission from galaxy SEDs; and the impact of galaxy inclination angle on dust attenuation laws.

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arXiv2020

Toward Enabling Reproducibility for Data-Intensive Research using the Whole Tale Platform

Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community. Tales are executable research objects that capture the code, data, and environment along with narrative and workflow information needed to re-create computational results from scientific studies. Creating reproducible research objects that enable reproducibility, transparency, and re-execution for computational experiments requiring significant compute resources or utilizing massive data is an especially challenging open problem. We describe opportunities, challenges, and solutions to facilitating reproducibility for data- and compute-intensive research, that we call "Tales at Scale," using the Whole Tale computing platform. We highlight challenges and solutions in frontend responsiveness needs, gaps in current middleware design and implementation, network restrictions, containerization, and data access. Finally, we discuss challenges in packaging computational experiment implementations for portable data-intensive Tales and outline future work.

cs.DC↗

arXiv2019

Cyberinfrastructure Requirements to Enhance Multi-messenger Astrophysics

The identification of the electromagnetic counterpart of the gravitational wave event, GW170817, and discovery of neutrinos and gamma-rays from TXS 0506+056 heralded the new era of multi-messenger astrophysics. As the number of multi-messenger events rapidly grow over the next decade, the cyberinfrastructure requirements to handle the increase in data rates, data volume, need for event follow up, and analysis across the different messengers will also explosively grow. The cyberinfrastructure requirements to enhance multi-messenger astrophysics will both be a major challenge and opportunity for astronomers, physicists, computer scientists and cyberinfrastructure specialists. Here we outline some of these requirements and argue for a distributed cyberinfrastructure institute for multi-messenger astrophysics to meet these challenges.

astro-ph.IM↗

arXiv2018

GAMER-2: a GPU-accelerated adaptive mesh refinement code -- accuracy, performance, and scalability

We present GAMER-2, a GPU-accelerated adaptive mesh refinement (AMR) code for astrophysics. It provides a rich set of features, including adaptive time-stepping, several hydrodynamic schemes, magnetohydrodynamics, self-gravity, particles, star formation, chemistry and radiative processes with GRACKLE, data analysis with yt, and memory pool for efficient object allocation. GAMER-2 is fully bitwise reproducible. For the performance optimization, it adopts hybrid OpenMP/MPI/GPU parallelization and utilizes overlapping CPU computation, GPU computation, and CPU-GPU communication. Load balancing is achieved using a Hilbert space-filling curve on a level-by-level basis without the need to duplicate the entire AMR hierarchy on each MPI process. To provide convincing demonstrations of the accuracy and performance of GAMER-2, we directly compare with Enzo on isolated disk galaxy simulations and with FLASH on galaxy cluster merger simulations. We show that the physical results obtained by different codes are in very good agreement, and GAMER-2 outperforms Enzo and FLASH by nearly one and two orders of magnitude, respectively, on the Blue Waters supercomputers using $1-256$ nodes. More importantly, GAMER-2 exhibits similar or even better parallel scalability compared to the other two codes. We also demonstrate good weak and strong scaling using up to 4096 GPUs and 65,536 CPU cores, and achieve a uniform resolution as high as $10{,}240^3$ cells. Furthermore, GAMER-2 can be adopted as an AMR+GPUs framework and has been extensively used for the wave dark matter ($ψ$DM) simulations. GAMER-2 is open source (available at https://github.com/gamer-project/gamer) and new contributions are welcome.

astro-ph.IM↗

arXiv2018

unyt: Handle, manipulate, and convert data with units in Python

Software that processes real-world data or that models a physical system must have some way of managing units. While simple approaches like the understood convention that all data are in a unit system (such as the MKS SI unit system) do work in practice, they are fraught with possible sources of error both by developers and users of the software. In this paper we present unyt, a Python library based on NumPy and SymPy for handling data that has units. It is designed both to aid quick interactive calculations and to be tightly integrated into a larger Python application or library. We compare unyt with two other Python libraries for handling units, Pint and astropy.units, and find that unyt is faster, has higher test coverage, and has fewer lines of code.

astro-ph.IM↗

arXiv2018

Computing Environments for Reproducibility: Capturing the "Whole Tale"

The act of sharing scientific knowledge is rapidly evolving away from traditional articles and presentations to the delivery of executable objects that integrate the data and computational details (e.g., scripts and workflows) upon which the findings rely. This envisioned coupling of data and process is essential to advancing science but faces technical and institutional barriers. The Whole Tale project aims to address these barriers by connecting computational, data-intensive research efforts with the larger research process--transforming the knowledge discovery and dissemination process into one where data products are united with research articles to create "living publications" or "tales". The Whole Tale focuses on the full spectrum of science, empowering users in the long tail of science, and power users with demands for access to big data and compute resources. We report here on the design, architecture, and implementation of the Whole Tale environment.

cs.CY↗

arXiv2018

Dwarf Galaxies with Ionizing Radiation Feedback. I: Escape of Ionizing Photons

We describe a new method for simulating ionizing radiation and supernova feedback in the analogues of low-redshift galactic disks. In this method, which we call star-forming molecular cloud (SFMC) particles, we use a ray-tracing technique to solve the radiative transfer equation for ultraviolet photons emitted by thousands of distinct particles on the fly. Joined with high numerical resolution of 3.8 pc, the realistic description of stellar feedback helps to self-regulate star formation. This new feedback scheme also enables us to study the escape of ionizing photons from star-forming clumps and from a galaxy, and to examine the evolving environment of star-forming gas clumps. By simulating a galactic disk in a halo of 2.3e11 Msun, we find that the average escape fraction from all radiating sources on the spiral arms (excluding the central 2.5 kpc) fluctuates between 0.08% and 5.9% during a ~20 Myr period with a mean value of 1.1%. The flux of escaped photons from these sources is not strongly beamed, but manifests a large opening angle of more than 60 degree from the galactic pole. Further, we investigate the escape fraction per SFMC particle, f_esc(i), and how it evolves as the particle ages. We discover that the average escape fraction f_esc is dominated by a small number of SFMC particles with high f_esc(i). On average, the escape fraction from a SFMC particle rises from 0.27% at its birth to 2.1% at the end of a particle lifetime, 6 Myrs. This is because SFMC particles drift away from the dense gas clumps in which they were born, and because the gas around the star-forming clumps is dispersed by ionizing radiation and supernova feedback. The framework established in this study brings deeper insight into the physics of photon escape fraction from an individual star-forming clump, and from a galactic disk.

astro-ph.GA↗

arXiv2018

Dwarf Galaxies with Ionizing Radiation Feedback. II: Spatially-resolved Star Formation Relation

We investigate the spatially-resolved star formation relation using a galactic disk formed in a comprehensive high-resolution (3.8 pc) simulation. Our new implementation of stellar feedback includes ionizing radiation as well as supernova explosions, and we handle ionizing radiation by solving the radiative transfer equation rather than by a subgrid model. Photoheating by stellar radiation stabilizes gas against Jeans fragmentation, reducing the star formation rate. Because we have self-consistently calculated the location of ionized gas, we are able to make spatially-resolved mock observations of star formation tracers, such as H-alpha emission. We can also observe how stellar feedback manifests itself in the correlation between ionized and molecular gas. Applying our techniques to the disk in a galactic halo of 2.3e11 Msun, we find that the correlation between star formation rate density (estimated from mock H-alpha emission) and molecular hydrogen density shows large scatter, especially at high resolutions of <~ 75 pc that are comparable to the size of giant molecular clouds (GMCs). This is because an aperture of GMC size captures only particular stages of GMC evolution, and because H-alpha traces hot gas around star-forming regions and is displaced from the molecular hydrogen peaks themselves. By examining the evolving environment around star clusters, we speculate that the breakdown of the traditional star formation laws of the Kennicutt-Schmidt type at small scales is further aided by a combination of stars drifting from their birthplaces, and molecular clouds being dispersed via stellar feedback.

astro-ph.GA↗

arXiv2018

The AGORA High-Resolution Galaxy Simulations Comparison Project. II: Isolated Disk Test

Using an isolated Milky Way-mass galaxy simulation, we compare results from 9 state-of-the-art gravito-hydrodynamics codes widely used in the numerical community. We utilize the infrastructure we have built for the AGORA High-resolution Galaxy Simulations Comparison Project. This includes the common disk initial conditions, common physics models (e.g., radiative cooling and UV background by the standardized package Grackle) and common analysis toolkit yt, all of which are publicly available. Subgrid physics models such as Jeans pressure floor, star formation, supernova feedback energy, and metal production are carefully constrained across code platforms. With numerical accuracy that resolves the disk scale height, we find that the codes overall agree well with one another in many dimensions including: gas and stellar surface densities, rotation curves, velocity dispersions, density and temperature distribution functions, disk vertical heights, stellar clumps, star formation rates, and Kennicutt-Schmidt relations. Quantities such as velocity dispersions are very robust (agreement within a few tens of percent at all radii) while measures like newly-formed stellar clump mass functions show more significant variation (difference by up to a factor of ~3). Systematic differences exist, for example, between mesh-based and particle-based codes in the low density region, and between more diffusive and less diffusive schemes in the high density tail of the density distribution. Yet intrinsic code differences are generally small compared to the variations in numerical implementations of the common subgrid physics such as supernova feedback. Our experiment reassures that, if adequately designed in accordance with our proposed common parameters, results of a modern high-resolution galaxy formation simulation are more sensitive to input physics than to intrinsic differences in numerical schemes.

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arXiv2016

Grackle: a Chemistry and Cooling Library for Astrophysics

We present the Grackle chemistry and cooling library for astrophysical simulations and models. Grackle provides a treatment of non-equilibrium primordial chemistry and cooling for H, D, and He species, including H2 formation on dust grains; tabulated primordial and metal cooling; multiple UV background models; and support for radiation transfer and arbitrary heat sources. The library has an easily implementable interface for simulation codes written in C, C++, and Fortran as well as a Python interface with added convenience functions for semi-analytical models. As an open-source project, Grackle provides a community resource for accessing and disseminating astrochemical data and numerical methods. We present the full details of the core functionality, the simulation and Python interfaces, testing infrastructure, performance, and range of applicability. Grackle is a fully open-source project and new contributions are welcome.

astro-ph.CO↗

arXiv2016

Machine Learning and Cosmological Simulations II: Hydrodynamical Simulations

We extend a machine learning (ML) framework presented previously to model galaxy formation and evolution in a hierarchical universe using N-body + hydrodynamical simulations. In this work, we show that ML is a promising technique to study galaxy formation in the backdrop of a hydrodynamical simulation. We use the Illustris Simulation to train and test various sophisticated machine learning algorithms. By using only essential dark matter halo physical properties and no merger history, our model predicts the gas mass, stellar mass, black hole mass, star formation rate, $g-r$ color, and stellar metallicity fairly robustly. Our results provide a unique and powerful phenomenological framework to explore the galaxy-halo connection that is built upon a solid hydrodynamical simulation. The promising reproduction of the listed galaxy properties demonstrably place ML as a promising and a significantly more computationally efficient tool to study small-scale structure formation. We find that ML mimics a full-blown hydrodynamical simulation surprisingly well in a computation time of mere minutes. The population of galaxies simulated by ML, while not numerically identical to Illustris, is statistically and physically robust and follows the same fundamental observational constraints. Machine learning offers an intriguing and promising technique to create quick mock galaxy catalogs in the future.

astro-ph.GA↗

arXiv2015

Machine Learning and Cosmological Simulations I: Semi-Analytical Models

We present a new exploratory framework to model galaxy formation and evolution in a hierarchical universe by using machine learning (ML). Our motivations are two-fold: (1) presenting a new, promising technique to study galaxy formation, and (2) quantitatively analyzing the extent of the influence of dark matter halo properties on galaxies in the backdrop of semi-analytical models (SAMs). We use the influential Millennium Simulation and the corresponding Munich SAM to train and test various sophisticated machine learning algorithms (k-Nearest Neighbors, decision trees, random forests and extremely randomized trees). By using only essential dark matter halo physical properties for haloes of $M>10^{12} M_{\odot}$ and a partial merger tree, our model predicts the hot gas mass, cold gas mass, bulge mass, total stellar mass, black hole mass and cooling radius at z = 0 for each central galaxy in a dark matter halo for the Millennium run. Our results provide a unique and powerful phenomenological framework to explore the galaxy-halo connection that is built upon SAMs and demonstrably place ML as a promising and a computationally efficient tool to study small-scale structure formation.

astro-ph.GA↗

arXiv2014

Dark Sky Simulations: Early Data Release

The Dark Sky Simulations are an ongoing series of cosmological N-body simulations designed to provide a quantitative and accessible model of the evolution of the large-scale Universe. Such models are essential for many aspects of the study of dark matter and dark energy, since we lack a sufficiently accurate analytic model of non-linear gravitational clustering. In July 2014, we made available to the general community our early data release, consisting of over 55 Terabytes of simulation data products, including our largest simulation to date, which used $1.07 \times 10^{12}~(10240^3)$ particles in a volume $8h^{-1}\mathrm{Gpc}$ across. Our simulations were performed with 2HOT, a purely tree-based adaptive N-body method, running on 200,000 processors of the Titan supercomputer, with data analysis enabled by yt. We provide an overview of the derived halo catalogs, mass function, power spectra and light cone data. We show self-consistency in the mass function and mass power spectrum at the 1% level over a range of more than 1000 in particle mass. We also present a novel method to distribute and access very large datasets, based on an abstraction of the World Wide Web (WWW) as a file system, remote memory-mapped file access semantics, and a space-filling curve index. This method has been implemented for our data release, and provides a means to not only query stored results such as halo catalogs, but also to design and deploy new analysis techniques on large distributed datasets.

astro-ph.CO↗

arXiv2014

The Birth of a Galaxy - III. Propelling reionisation with the faintest galaxies

Starlight from galaxies plays a pivotal role throughout the process of cosmic reionisation. We present the statistics of dwarf galaxy properties at z > 7 in haloes with masses up to 10^9 solar masses, using a cosmological radiation hydrodynamics simulation that follows their buildup starting with their Population III progenitors. We find that metal-enriched star formation is not restricted to atomic cooling ($T_{\rm vir} \ge 10^4$ K) haloes, but can occur in haloes down to masses ~10^6 solar masses, especially in neutral regions. Even though these smallest galaxies only host up to 10^4 solar masses of stars, they provide nearly 30 per cent of the ionising photon budget. We find that the galaxy luminosity function flattens above M_UV ~ -12 with a number density that is unchanged at z < 10. The fraction of ionising radiation escaping into the intergalactic medium is inversely dependent on halo mass, decreasing from 50 to 5 per cent in the mass range $\log M/M_\odot = 7.0-8.5$. Using our galaxy statistics in a semi-analytic reionisation model, we find a Thomson scattering optical depth consistent with the latest Planck results, while still being consistent with the UV emissivity constraints provided by Ly$α$ forest observations at z = 4-6.

astro-ph.CO↗

arXiv2013

The AGORA High-Resolution Galaxy Simulations Comparison Project

We introduce the AGORA project, a comprehensive numerical study of well-resolved galaxies within the LCDM cosmology. Cosmological hydrodynamic simulations with force resolutions of ~100 proper pc or better will be run with a variety of code platforms to follow the hierarchical growth, star formation history, morphological transformation, and the cycle of baryons in and out of 8 galaxies with halo masses M_vir ~= 1e10, 1e11, 1e12, and 1e13 Msun at z=0 and two different ("violent" and "quiescent") assembly histories. The numerical techniques and implementations used in this project include the smoothed particle hydrodynamics codes GADGET and GASOLINE, and the adaptive mesh refinement codes ART, ENZO, and RAMSES. The codes will share common initial conditions and common astrophysics packages including UV background, metal-dependent radiative cooling, metal and energy yields of supernovae, and stellar initial mass function. These are described in detail in the present paper. Subgrid star formation and feedback prescriptions will be tuned to provide a realistic interstellar and circumgalactic medium using a non-cosmological disk galaxy simulation. Cosmological runs will be systematically compared with each other using a common analysis toolkit, and validated against observations to verify that the solutions are robust - i.e., that the astrophysical assumptions are responsible for any success, rather than artifacts of particular implementations. The goals of the AGORA project are, broadly speaking, to raise the realism and predictive power of galaxy simulations and the understanding of the feedback processes that regulate galaxy "metabolism." The proof-of-concept dark matter-only test of the formation of a galactic halo with a z=0 mass of M_vir ~= 1.7e11 Msun by 9 different versions of the participating codes is also presented to validate the infrastructure of the project.

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