Enzo: An Adaptive Mesh Refinement Code for Astrophysics

Abstract

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 1, 2, and 3 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 code's parallel performance, and discuss the Enzo collaboration's code development methodology.

60 pages, 22 figures, submitted to ApJS. The code is available at http://enzo-project.org

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• Positive or Negative? The Impact of X-ray Feedback on the Formation of Direct Collapse Black Hole Seeds
• Direct-collapse black hole formation induced by internal radiation of host halos
• It's a Breeze: The Circumgalactic Medium of a Dwarf Galaxy is Easy to Strip
• The formation of the primitive star SDSS J102915+172927: effect of the dust mass and the grain-size distribution
• GMC Evolution in a Barred Spiral Galaxy with Star Formation and Thermal Feedback
• The Borg Cube Simulation: Cosmological Hydrodynamics with CRK-SPH
• A scalable elliptic solver with task-based parallelism for the SpECTRE numerical relativity code
• Denoising Diffusion Probabilistic Models to Predict the Density of Molecular Clouds
• On the Piecewise Parabolic Method for Compressible Flow with Stellar Equations of State
• A general-purpose timestep criterion for simulations with gravity
• Classifying and modelling spiral structures in hydrodynamic simulations of astrophysical discs
• Simulations of Galaxy Cluster Collisions with a Dark Plasma Component
• Calibration of a star formation and feedback model for cosmological simulations with Enzo
• Redshift estimates for fast radio bursts and implications on intergalactic magnetic fields
• Radio-flaring Ultracool Dwarf Population Synthesis
• Probing the Dependence of the Intergalactic Medium on Large Scale Environment Using the Low Redshift Lyman Alpha Forest
• The Robustness of Cosmological Hydrodynamic Simulation Predictions to Changes in Numerics and Cooling Physics
• Cosmic Ray Driven Outflows in an Ultraluminous Galaxy
• Using H$\alpha$ Filaments to Probe AGN Feedback in Galaxy Clusters
• On the effect of Lyman alpha trapping during the initial collapse of massive black hole seeds
• Initial conditions for cosmological N-body simulations of the scalar sector of theories of Newtonian, Relativistic and Modified Gravity
• The Effects of Ram Pressure on the Cold Clouds in the Centers of Galaxy Clusters
• Simplified galaxy formation with mesh-less hydrodynamics
• Radiation-driven turbulent accretion onto massive black holes
• An estimate of the stochastic gravitational wave background from the MassiveBlackII simulation
• Hints of Primordial Magnetic Fields at Recombination and Implications for the Hubble Tension
• The effect of dark matter resolution on the collapse of baryons in high redshift numerical simulations
• Intermittent fragmentation and statistical variations during gas collapse in magnetised atomic cooling haloes
• On the complexity and the information content of cosmic structures
• Turbulent magnetic fields in merging clusters: A case study of Abell 2146
• Multidimensional Simulations of Core Convection
• Cosmic magnetic fields with MASCLET: an application to galaxy clusters
• Perfectly parallel cosmological simulations using spatial comoving Lagrangian acceleration
• Radio Power from Direct-Collapse Black Holes
• Role of magnetic fields in the formation of direct collapse black holes
• The evolution of cosmic ray electrons in the cosmic web: seeding by AGN, star formation and shocks
• Effects of Galactic Disc Inclination and Resolution on Observed GMC Properties and Larson's Scaling Relations
• Multi wavelength cross-correlation analysis of the simulated cosmic web
• First emergence of cold accretion and supermassive star formation in the early universe
• Fast cloud-cloud collisions in a strongly barred galaxy: Suppression of massive star formation
• Connection among environment, cloud-cloud collision speed, and star formation activity in the strongly barred galaxy NGC1300
• An intergalactic medium temperature from a giant radio galaxy
• Massive black hole formation in Population III star clusters
• Gas Accretion and Angular Momentum
• Formation of First Galaxies inside Density Peaks and Voids under the Influence of Dark Matter-Baryon Streaming Velocity, I: Initial Condition and Simulation Scheme
• Post-dynamical inspiral phase of common envelope evolution. The role of magnetic fields
• Gas around galaxy haloes: methodology comparisons using hydrodynamical simulations of the intergalactic medium
• Fragmentation in Population III Galaxies formed through Ionizing Radiation
• FORECAST: a flexible software to forward model cosmological hydrodynamical simulations mimicking real observations
• Magnetohydrodynamics with GAMER
• Signature of Supersonic Turbulence in Galaxy Clusters Revealed by AGN-driven H$\alpha$ Filaments
• Orbital Migration of Protoplanets in a Marginally Gravitationally Unstable Disk. II. Migration, Merging, and Ejection
• Gravitational Fragmentation of Extremely Metal-poor Circumstellar Discs
• Dynamics and Morphology of Cold Gas in Fast, Radiatively Cooling Outflows: Constraining AGN Energetics with Horseshoes
• If dark matter is fuzzy, the first stars form in massive pancakes
• Efficient radial migration by giant molecular clouds in the first several hundred Myr after the stellar birth
• Cinematic Visualization of Multiresolution Data: Ytini for Adaptive Mesh Refinement in Houdini
• Fully Coupled Simulation of Cosmic Reionization. III. Stochastic Early Reionization by the Smallest Galaxies
• Unveiling the role of galactic rotation on star formation
• On the Mass Loading of AGN-Driven Outflows in Elliptical Galaxies and Clusters
• Modeling gravitational instabilities in self-gravitating protoplanetary disks with adaptive mesh refinement techniques
• Formation of Pop II star clusters in the aftermath of a pair instability supernova
• A fast tree-based method for estimating column densities in Adaptive Mesh Refinement codes Influence of UV radiation field on the structure of molecular clouds
• Collapse and Fragmentation of Magnetic Molecular Cloud Cores with the Enzo AMR MHD Code. II. Prolate and Oblate Cores
• Mesh-free hydrodynamics in PKDGRAV3 for galaxy formation simulations
• Direct Collapse to Supermassive Black Hole Seeds: Comparing the AMR and SPH Approaches
• The AGORA High-Resolution Galaxy Simulations Comparison Project VII: Satellite quenching in zoom-in simulation of a Milky Way-mass halo
• Connecting Primordial Star Forming Regions and Second Generation Star Formation in the Phoenix Simulations
• A multishock scenario for the formation of radio relics
• Deuterium Chemodynamics of Massive Pre-Stellar Cores
• MAGNUS: A new resistive MHD code with heat flow terms
• Collapsing Molecular Clouds with Tracer Particles: Part I, What Collapses?
• Origin and Evolution of Structure and Nucleosynthesis for Galaxies in the Local Group
• Intergalactic medium rotation measure of primordial magnetic fields
• The Interstellar Medium and Star Formation in Local Galaxies: Variations of the Star Formation Law in Simulations
• Massive core/star formation triggered by cloud-cloud collision: II High-speed collisions of magnetized clouds
• Conformal invariance of weakly compressible two-dimensional turbulence
• First Star Formation in the Presence of Primordial Magnetic Fields
• Manufacturing cosmic rays in the evolving dynamical states of galaxy clusters
• Induced metal-free star formation around a massive black hole seed
• MHD simulations of dense core collision
• A morphological analysis of the substructures in radio relics
• Legolas 2.0: Improvements and extensions to an MHD spectroscopic framework
• On the alignment of haloes, filaments and magnetic fields in the simulated cosmic web
• C IV and He II Line Emission of Lyman Alpha Blobs: Powered by Shock Heated Gas
• Formation and evolution of the local interstellar environment: combined constraints from nucleosynthetic and X-ray data
• An uncertainty principle for star formation -- V. The influence of dust extinction on star formation rate tracer lifetimes and the inferred molecular cloud lifecycle
• Radio-relic and the diffuse emission trail discovered in a low mass galaxy cluster Abell 1697
• Inflationary and phase-transitional primordial magnetic fields in galaxy clusters
• Structure-preserving finite-element schemes for the Euler-Poisson equations
• When Gas Dynamics Decouples from Galactic Rotation: Characterizing ISM Circulation in Disk Galaxies
• Amplification of Magnetic Fields in a Primordial HII Region and Supernova
• Turbulent Pressure Support in Galaxy Clusters -- Impact of the Hydrodynamical Solver
• Density and Velocity Correlations in Isothermal Supersonic Turbulence
• Influence of adaptive mesh refinement and the hydro solver on shear-induced mass stripping in a minor-merger scenario
• Aeos: Transport of Metals from Minihalos following Population III Stellar Feedback
• Biconical-dominated Accretion Flow onto Seed Black Holes in a Hyper-accretion Regime
• Three- and two-point spatial correlations of IGM at $z\sim 2$: Cloud based analysis using simulations
• The impact of the cosmological constant on past and future star formation
• Seeking Self-Regulating Simulations of Idealized Milky Way-Like Galaxies
• A fast dynamic smooth adaptive meshing scheme with applications to compressible flow
• Saturation level of turbulence in collapsing gas clouds
• Magrathea-Pathfinder: A 3D adaptive-mesh code for geodesic ray tracing in $N$-body simulations
• Atmospheric Circulation in Simulations of the AGN-CGM Connection at Halo Masses $\sim 10^{13.5},M_{\odot }$
• An adaptive particle-mesh gravity solver for ENZO
• Hungry or Not: How Stellar-Mass Black Holes Grow (or Don't) in Dark Matter Mini-Haloes at High-Resolution
• An Application of Gaussian Process Modeling for High-order Accurate Adaptive Mesh Refinement Prolongation
• Psi-GAN: A power-spectrum-informed generative adversarial network for the emulation of large-scale structure maps across cosmologies and redshifts
• On the impact of AGN feedback modes onto the turbulent properties of the multiphase ICM
• Smart Adaptive Mesh Refinement with NEMoSys
• How complex is the cosmic web?
• Blue galaxies: modelling nebular He II emission in high redshift galaxies
• WENO-Wombat: Scalable Fifth-Order Constrained-Transport Magnetohydrodynamics for Astrophysical Applications
• Numerical cosmology on the GPU with Enzo and Ramses
• Enabling Radiative Transfer on AMR grids in CRASH
• Dynamical Evolution of an Ultra-relativistic Fireball Colliding with a Freely Expanding Gas
• Cosmological simulations of the generation of cluster-scale radio emission from turbulent re-acceleration
• Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback?
• Temporal Self-Organization in Galaxy Formation
• Honing and proofing Astrophysical codes on the road to Exascale. Experiences from code modernization on many-core systems
• Accelerated growth of seed black holes by dust in the early universe
• Suppression of H2-cooling in protogalaxies aided by trapped Lyα cooling radiation
• Dark-ages Reionization and Galaxy Formation Simulation - XV. Stellar evolution and feedback in dwarf galaxies at high redshift
• Understanding biases in measurements of molecular cloud kinematics using line emission
• Multi-Epoch Machine Learning 2: Identifying physical drivers of galaxy properties in simulations
• The Physical Nature of the Most Metal-Poor Damped Lyman Alpha Systems
• The SRG/eROSITA All-Sky Survey: Large-scale view of the Centaurus cluster
• Massively Parallel Computation of Accurate Densities for N-body Dark Matter Simulations using the Phase-Space-Element Method
• Growth of Light Seed Black Holes in the Early Universe
• Evolution of Star Cluster Within Galaxy using Self-consistent Hybrid Hydro/N-body Simulation
• CRexit: how different cosmic ray transport modes affect thermal instability in the circumgalactic medium
• Finite shock model of density in supersonic turbulence
• Touching the Stars: Using High-Resolution 3D Printing to Visualize Stellar Nurseries
• A comparison of numerical methods for computing the reionization of intergalacitc hydrogen and helium by a central radiating source
• Reconstructing the genesis of a globular cluster system at a look-back time of 9.1 Gyr with the JWST
• Growth of A Massive Black Hole Via Tidal Disruption Accretion
• The Impact of Baryons on the Large-Scale Structure of the Universe
• Gaseous Dynamical Friction: a Numerical Study of Extended Perturbers
• Predicting Localized Primordial Star Formation with Deep Convolutional Neural Networks
• Impact of Population III stars on the astrophysical gravitational-wave background
• The AGORA High-resolution Galaxy Simulations Comparison Project. X: Formation and Evolution of Galaxies at the High-redshift Frontier
• The Case for Hot-Mode Accretion in Abell 2029
• Direct Collapse Accretion Disks Within Dark Matter Halos: Saturation of the Magnetorotational Instability and the Field Expulsion
• Machine-guided Exploration and Calibration of Astrophysical Simulations
• On the interpretation of XRISM X-ray measurements of turbulence in the intracluster medium: a comparison with cosmological simulations
• Field-Level Comparison and Robustness Analysis of Cosmological N-body Simulations
• Simulating Radiative Magnetohydrodynamical Flows with AstroBEAR: Implementation and Applications of Non-equilibrium Cooling
• Boundary conditions in hydrodynamic simulations of isolated galaxies and their impact on the gas-loss processes
• OVI Emission From the Supernovae-regulated Interstellar Medium: Simulation Vs Observation
• Joint inference on the redshift distribution of fast radio burst and on the intergalactic baryon content
• Clusternets: A deep learning approach to probe clustering dark energy
• Tests of AGN Feedback Kernels in Simulated Galaxy Clusters
• Triggered Population III star formation: the effect of H${}_2$ self-shielding
• 3-3-1 Self Interacting Dark Matter and the Galaxy Core-Cusp problem
• Simulated Rotation Measure Sky from Primordial Magnetic Fields
• The Coma cluster at LOFAR frequencies II: the halo, relic, and a new accretion relic
• Slow Cooling in Low Metallicity Clouds: An Origin of Globular Cluster Bimodality?
• Direct Collapse to Precursors of Supermassive Black Hole Seeds:Radiation-feedback-generated Outflows
• Pseudo-spectral solver versus grid-based solver: A quantitative accuracy test using GMHD3D and PLUTO4.4
• Mapping Diffuse Radio Sources Using TUNA: A Transformer-Based Deep Learning Approach
• SIGAME v3: Gas Fragmentation in Post-processing of Cosmological Simulations for More Accurate Infrared Line Emission Modeling
• Aeos: The Impact of Population III Initial Mass Function and Star-by-Star Models in Galaxy Simulations
• Comparison of two different integration methods for the (1+1)-Dimensional Schrödinger-Poisson Equation
• The Complexity and Information Content of Simulated Universes
• Visualization in Astrophysics: Developing New Methods, Discovering Our Universe, and Educating the Earth
• A New Residual Distribution Hydrodynamics Solver for Astrophysical Simulations
• An Observationally Driven Multifield Approach for Probing the Circum-Galactic Medium with Convolutional Neural Networks
• Gas Inflow and Star Formation near Supermassive Black Holes: The Role of Nuclear Activity
• Convolutional Deep Denoising Autoencoders for Radio Astronomical Images
• Reduced Gas Accretion onto Galaxies due to Effects of External Giant Radio Lobes
• A Hierarchical Shock Model of Ultra-High-Energy Cosmic Rays
• LightAMR format standard and lossless compression algorithms for adaptive mesh refinement grids: RAMSES use case
• Software Abstractions and Methodologies for HPC Simulation Codes on Future Architectures
• A fast algorithm for identifying Friends-of-Friends halos
• Origin of Weak MgII and Higher Ionization Absorption Lines in an Outflow from an Intermediate-Redshift Dwarf Satellite Galaxy
• What goes around comes around: the fate of stars in stripped tails of gas
• Computational Fluid Dynamics with the Coupled Discrete Unified Gas Kinetic Scheme (CDUGKS)
• Numerical Methods for Simulating Star Formation
• Extended Hernquist-Springel formalism for cosmic star formation
• Gravitational Self-force Errors of Poisson Solvers on Adaptively Refined Meshes
• Effect of cosmic rays and ionizing radiation on observational ultraviolet plasma diagnostics in the circumgalactic medium
• Adaptive friends-of-friends algorithm for identifying gravitationally bound cosmological structures
• Cosmological simulation of a radio synchrotron bridge between pre-merging galaxy clusters
• Gravitational-Wave Signatures of Massive Black Hole Formation
• Turbulence in the intragroup and circumgalactic medium
• Inflow Generated X-ray Corona Around Supermassive Black Holes and Unified Model for X-ray Emission
• Transferring Data from a Voronoi Mesh to an Adaptive Cartesian Grid in Pursuit of Self-consistent Top-down Star Formation
• Hydromagnetic waves in an expanding universe -- cosmological MHD code tests using analytic solutions
• The 21-cm signature of X-ray heated halos around galaxies during cosmic dawn
• Magnetic field and kinetic helicity evolution in simulations of interacting disk galaxies
• Ginnungagap -- a massively parallel cosmological initial conditions generator
• Modelling the Energy Spectra of Radio Relics
• From Dark Matter Minihalos to Large-Scale Radiative Feedback: A Self-Consistent 3D Simulation of the First Stars and Galaxies using Neural Networks
• Simulating High-Velocity Clouds in the Observational Plane: An Initial Study with the Smith Cloud
• Periodic I/O scheduling for super-computers
• Cosmological Analysis with Calibrated Neural Quantile Estimation and Approximate Simulators
• Kinematic dynamos and resolution limits for Smoothed Particle Magnetohydrodynamics
• Validating the CROCODILE model within the AGORA galaxy simulation framework
• libyt: an In Situ Interface Connecting Simulations with yt, Python, and Jupyter Workflows
• Redshift effects implications on revised models of Stephan's quintet
• Identification of Candidate Halos Hosting Massive Black Hole Seeds in the $\text{Renaissance}$ Simulations with Support Vector Machines
• Time-dependent adaptive mesh refinement solver for the Gross-Pitaevskii-Poisson equations
• Extragalactic Sources and Propagation of UHECRs
• Imladris: a detailed and flexible model for galaxy simulations with individual stars
• Variational autoencoder for generating realistic $N$-body simulations for dark matter halos
• Direct Collapse Pre-supermassive Black Hole Objects as Ly$\alpha$ Emitters
• CAFE-AMR: A computational MHD Solar Physics simulation tool that uses AMR