3D-PDR: A new three-dimensional astrochemistry code for treating Photodissociation Regions
arXiv:1209.1091 · doi:10.1111/j.1365-2966.2012.22077.x
Abstract
Photodissociation regions (PDRs) define the transition zone between an ionized and a dark molecular region. They consist of neutral gas which interacts with far-ultraviolet radiation and are characterized by strong infrared line emission. Various numerical codes treating one-dimensional PDRs have been developed in the past, simulating the complexity of chemical reactions occurring and providing a better understanding of the structure of a PDR. In this paper we present the three-dimensional code, 3D-PDR, which can treat PDRs of arbitrary density distribution. The code solves the chemistry and the thermal balance self-consistently within a given three-dimensional cloud. It calculates the total heating and cooling functions at any point in a given PDR by adopting an escape probability method. It uses a HEALPix-based ray-tracing scheme to evaluate the attenuation of the far-ultraviolet radiation in the PDR and the propagation of the far-infrared/submm line emission out of the PDR. We present benchmarking results and apply 3D-PDR to i) a uniform-density spherical cloud interacting with a plane-parallel external radiation field, ii) a uniform-density spherical cloud interacting with a two-component external radiation field, and iii) a cometary globule interacting with a plane-parallel external radiation field. We find that the code is able to reproduce the benchmarking results of various other one-dimensional numerical codes treating PDRs. We also find that the accurate treatment of the radiation field in the fully three-dimensional treatment of PDRs can in some cases leads to different results when compared to a standard one-dimensional treatment.
19 pages, 11 figures, accepted for publication in MNRAS
References in corpus (14)
- Simulating the formation of molecular clouds. I. Slow formation by gravitational collapse from static initial conditions
- Simulating the formation of molecular clouds. II. Rapid formation from turbulent initial conditions
- [CII] 158m Emission and Metallicity in PDRs
- The HII Region of a Primordial Star
- Magnetohydronamic Evolution of HII Regions in Molecular Clouds: Simulation Methodology, Tests, and Uniform Media
- Molecular line intensities as measures of cloud masses - I. Sensitivity of CO emissions to physical parameter variations
- The ISM in spiral galaxies: can cooling in spiral shocks produce molecular clouds?
- iVINE - Ionization in the parallel tree/SPH code VINE: First results on the observed age-spread around O-stars
- Chemical Rates on Small Grains and PAHs: C^+ Recombination and H_2 Formation
- Smoothed Particle Hydrodynamics simulations of expanding HII regions. I. Numerical methods and tests
- Multidimensional chemical modelling, II. Irradiated outflow walls
- A clumpy-cloud PDR model of the global far-infrared line emission of the Milky Way
- Sensitivity of PDR Calculations to Microphysical Details
- Clumpy photon-dominated regions in Carina. I. [CI] and mid-J CO lines in two 4'x4' fields
Cited by in corpus (83)
- HI-to-H2 Transitions and H I Column Densities in Galaxy Star-Forming Regions
- Photodissociation and X-Ray Dominated Regions
- The Green Bank Ammonia Survey (GAS): First Results of NH3 mapping the Gould Belt
- Deriving a multivariate CO-to-H conversion function using the [CII]/CO(1-0) ratio and its application to molecular gas scaling relations
- Effective destruction of CO by cosmic rays: implications for tracing H gas in the Universe
- External photoevaporation of protoplanetary discs in sparse stellar groups: the impact of dust growth
- UCLCHEM: A Gas-Grain Chemical Code
- ALMA observations of atomic carbon in z~4 dusty star-forming galaxies
- Cosmic-ray induced destruction of CO in star-forming galaxies
- Is atomic carbon a good tracer of molecular gas in metal-poor galaxies?
- The properties of the interstellar medium of galaxies across time as traced by the neutral atomic carbon [CI]
- Analytic HI-to-H2 Photodissociation Transition Profiles
- An Alternative Accurate Tracer of Molecular Clouds: The "-Factor"
- Zooming in on Individual Star Formation: Low- and High-mass Stars
- The first multi-dimensional view of mass loss from externally FUV irradiated protoplanetary discs
- Using CO line ratios to trace the physical properties of molecular clouds
- New places and phases of CO-poor/CI-rich molecular gas in the Universe
- An ALMA multi-line survey of the ISM in two quasar host-companion galaxy pairs at
- Chemistry and radiative shielding in star forming galactic disks
- Molecular clouds photoevaporation and FIR line emission
- Photodissociation Region Diagnostics Across Galactic Environments
- GMC Collisions as Triggers of Star Formation. V. Observational Signatures
- A dense, solar metallicity ISM in the z=4.2 dusty star-forming galaxy SPT0418-47
- Where can a Trappist-1 planetary system be produced?
- Grand challenges in protoplanetary disc modelling
- CO-dark gas and molecular filaments in Milky Way-type galaxies - II: The temperature distribution of the gas
- The Astrochemical Impact of Cosmic Rays in Protoclusters I: Molecular Cloud Chemistry
- Does the CO-to-H2 conversion factor depend on the star formation rate?
- Modelling clumpy PDRs in 3D - Understanding the Orion Bar stratification
- Diagnostics of the molecular component of PDRs with mechanical heating. II: line intensities and ratios
- TORUS-3DPDR: A self-consistent code treating three-dimensional photoionization and photodissociation regions
- Synthetic observations of star formation and the interstellar medium
- Radiative transfer meets Bayesian statistics: where does a galaxy's [CII] emission come from?
- Modeling the Atomic-to-Molecular Transition and Chemical Distributions of Turbulent Star-Forming Clouds
- Synthetic [CII] emission maps of a simulated molecular cloud in formation
- Photochemical-dynamical models of externally FUV irradiated protoplanetary discs
- A simple model for molecular hydrogen chemistry coupled to radiation hydrodynamics
- On the relative importance of different microphysics on the D-type expansion of galactic HII regions
- PDFchem: A new fast method to determine ISM properties and infer environmental parameters using probability distributions
- Magritte, a modern software library for 3D radiative transfer: I. Non-LTE atomic and molecular line modelling
- Bright Extragalactic ALMA Redshift Survey (BEARS) III: Detailed study of emission lines from 71 Herschel targets
- Simulating the atomic and molecular content of molecular clouds using probability distributions of physical parameters
- A multiwavelength study of the Magellanic-type galaxy NGC 4449 - I. Modelling the spectral energy distribution, the ionization structure and the star formation history
- The Inception of Star Cluster Formation Revealed by [CII] Emission Around an Infrared Dark Cloud
- Surface chemistry in photodissociation regions
- The impact of cosmic-ray attenuation on the carbon cycle emission in molecular clouds
- DART-Ray: a 3D ray-tracing radiative transfer code for calculating the propagation of light in dusty galaxies
- Self-consistent dust and non-LTE line radiative transfer with SKIRT
- Dust delivery and entrainment in photoevaporative winds
- Astrochemical Correlations in Molecular Clouds
- The Observational Anatomy of Externally Photoevaporating Planet-Forming Discs I: Atomic Carbon
- Molecular clumps photoevaporation in ionized regions
- The Interstellar Medium Properties of Heavily Reddened Quasars & Companions at z~2.5 with ALMA & JVLA
- The origin of the [CII]-deficit in a simulated dwarf galaxies starburst
- The KOSMA- PDR Model -- I. Recent updates to the numerical model of photo-dissociated regions
- Assessing molecular line diagnostics of triggered star formation using synthetic observations
- Magritte, a modern software library for 3D radiative transfer: II. Adaptive ray-tracing, mesh construction and reduction
- Dependence of Chemical Abundance on the Cosmic Ray Ionization Rate in IC 348
- The Astrochemical Impact of Cosmic Rays in Protoclusters II: CI-to-H and CO-to-H Conversion Factors
- SUNRISE: The rich molecular inventory of high-redshift dusty galaxies revealed by broadband spectral line surveys
- A Photodissociation Region study of NGC 4038
- Abundance ratios of OH/CO and HCO+/CO as probes of the cosmic ray ionization rate in diffuse clouds
- The chemical footprint of the star formation feedback in M 82 on scales of 100 pc
- Star Cluster Formation in Orion A
- The CO-dark molecular gas in the cold HI arc
- A new analytic approach to infer the cosmic-ray ionization rate in hot molecular cores from HCO, NH, and CO observations
- Cosmic-ray-induced H line emission: Astrochemical modeling and implications for JWST observations
- Assessing the Impact of Astrochemistry on Molecular Cloud Turbulence Statistics
- Metallicity dependence of the CO-to-H and the [CI]-to-H conversion factors in galaxies
- A PDR model for the FIR mid- CO ladder with universal rotational temperature in star forming region
- Applying a one-dimensional PDR model to the Taurus molecular cloud and its atomic envelope
- Distribution of Water Vapor in Molecular Clouds. II
- A Hydrochemical Hybrid Code for Astrophysical Problems. I. Code Verification and Benchmarks for Photon-Dominated Region (PDR)
- A Model for Protostellar Cluster Luminosities and the Impact on the CO-H Conversion Factor
- Mapping the Cosmic-Ray Ionization Rate in the Local Galaxy with H
- Astrochemistry in external galaxies: how to use molecules as probes of their physical conditions
- High Resolution Observations of HI in the IC 63 Reflection Nebula
- DESHIMA 2.0: Rapid redshift surveys and multi-line spectroscopy of dusty galaxies
- An analytic formalism to describe the - relationship in molecular clouds
- NeuralPDR: Neural Differential Equations as surrogate models for Photodissociation Regions
- A Probabilistic Model to Estimate Number Densities from Column Densities in Molecular Clouds
- The impact of attenuation on cosmic-ray chemistry: I. Abundances and chemical calibrators in molecular clouds
- Topological models to infer multiphase interstellar medium properties