Introducing Enzo, an AMR Cosmology Application

Alexei Kritsuk; Brian W. O'Shea; Greg Bryan; James Bordner; Michael L. Norman; Robert Harkness; Tom Abel

REVIEW

Introducing Enzo, an AMR Cosmology Application

Brian W. O'Shea, Greg Bryan, James Bordner, Michael L. Norman, Tom Abel, Robert Harkness, Alexei Kritsuk

Astrophysics · Submitted 1 Mar 2004 · 15 references

Pith's verdict: A tool-release paper, not a science result: Enzo is real and became a standard AMR cosmology code, but §3's comparison with Lagrangian codes is asserted without any supporting curve.

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arXiv IDastro-ph/0403044 (version 1)

Pith ID3DZFQLV6, Pith's permanent record of this paper and its review

CitationAlexei Kritsuk, Brian W. O'Shea, Greg Bryan, James Bordner, Michael L. Norman, Robert Harkness, Tom Abel. "Introducing Enzo, an AMR Cosmology Application." arXiv:astro-ph/0403044 (2004). https://pith.science/paper/3DZFQLV6

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Editor's note

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Short version: this is a tool-release paper, not a science result, and it should be read that way. Enzo is real, it was downloadable, and it became one of the standard AMR cosmology codes. That is the contribution, and it is a genuine one — a portable MPI-parallel 3D Eulerian AMR code with particle-mesh dark matter, PPM hydro, cooling, UV background, and star formation, released to the community. Credit where it is earned: shipping working, portable code that other groups actually run is harder and more useful than most of what appears in these proceedings volumes, and it is checkable evidence in a way that a claimed number is not. What is new here is integration and availability, not algorithms. AMR is Berger-Colella [2], PPM is Woodward-Colella [7] with the cosmological adaptation in Bryan et al. [8], Zeus is [9,10], the 28-species chemistry is Abel/Anninos [11,12], the UV background is Haardt-Madau [14], star formation is Cen-Ostriker [15]. The authors say so plainly, which I appreciate. The data-structure description in §2.1 — real versus ghost grids, three-deep ghost zones, linked-list hierarchy, per-level load balancing — is the most useful part and is specific enough to be informative. Soft spots, in order of how much they matter. §3 is the weakest section. The claim that low-density cells are well-resolved, 'in stark contrast to simulations performed using Lagrangian methods, which are typically undersampled at low density,' has no SPH curve anywhere in Figures 2-4; both codes shown are Eulerian. That comparison is asserted, not shown. Related: the text says mean cell mass 'stays fairly constant' with overdensity and then describes a trend — lower in underdense, higher in overdense. Pick one. And the run parameters, cosmology, starting redshift, refinement criteria, are never tabulated, so the '5-10 times better' numbers cannot be reproduced from the text. I would push back on the reader's weakest-assumption call. The one-sentence gravity description in §2.2 summarizes methods implemented and documented in [3]-[6]; the paper does not claim a convergence result for that solver, so the absence of a cross-level consistency study is a documentation gap, not a hole in what is being claimed. The place the text actually outruns its evidence is §3, as above. There is no verification suite of its own; hydro accuracy rests on [8] and performance on Bordner's companion piece. For a proceedings introduction that is acceptable, but a reader who wants to trust the solver has to go elsewhere. Who it is for: someone deciding whether to use Enzo, or wanting a citable description of its architecture. Not a source for validation evidence. Peer review: yes, send it out. Code-release papers deserve referee time, and this one is load-bearing for a lot of later literature. Expect the referee to ask for the §3 fixes and a table of run parameters.

Referee report

Significance

The significance of this contribution is as a citable description of a widely used, publicly released community code rather than as a report of a new physical result. The strengths worth naming explicitly are: the code is genuinely public and downloadable, which is a substantive contribution to the field; the method descriptions in Sections 2.1 through 2.4 are specific enough to be usable (solver choices, ghost-zone depth, refinement criteria, the dual-energy formalism motivated by hypersonic cosmological flows, and the decoupling of the fast H- and H2+ reactions from the 28-equation primordial chemistry network); the physics framework is described as extensible, with the cooling, ultraviolet background, and star formation modules presented as pluggable; and the portability claim is backed by a concrete list of machines. The paper is also candid about what it does not cover, deferring performance and optimization to the companion Bordner contribution in the same volume. If the code performs as described, the paper's value is durable: it gives users and citers a single reference for what Enzo solves and how.

Major objections (3)

[§3, paragraph 1 (with Figures 2-4)] The sentence stating that low-density cells 'are well-resolved in these simulations, which is in stark contrast to simulations performed using Lagrangian methods, which are typically undersampled at low density' is a comparative claim that no figure in the paper supports. Figures 2, 3 and 4 contain only Eulerian runs (Enzo PPM, Enzo Zeus, and the high-overdensity-threshold variant); there is no smoothed-particle-hydrodynamics curve anywhere in the manuscript. Either add an SPH comparison run to Figure 2 or restrict the sentence to what the figures show, namely that the Eulerian AMR runs populate the full density range down to low overdensity. As written, a reader will take the contrast as a demonstrated result of this paper.
[§3, paragraphs 1-3] The quantitative statements in Section 3 ('the total number of cells at the end of the run has increase[d] by a factor of ~8-10', 'the mean mass resolution ... increases by almost an order of magnitude', 'between ~5-10 times better than the starting mass resolution') are attributed to a 'representative suite' whose parameters are never tabulated. The text gives root grid sizes (64^3 or 128^3), 5 or 6 refinement levels, refinement factors of 2.0, and overdensity thresholds of 4.0 (dark matter) and 2.0 (baryons), but it does not state which combination belongs to which labelled run, nor the cosmology, box size in comoving units, starting redshift, dark matter particle number per run, or the redshift at which the statistics are taken. Without a parameter table these numbers cannot be checked or reproduced, which matters because they are the paper's only quantitative results. A short table mapping each figure label to its root grid, level count, particle number, threshold, and output redshift would resolve this.
[§3, paragraph 3 and Figure 4] The description of Figure 4 is internally inconsistent. The text says the mean cell mass as a function of overdensity 'stays fairly constant', and in the same sentence says there are 'lower mean cell masses in underdense regions and higher mean cell masses in highly overdense regions', which is a statement of variation, not constancy. The Figure 4 caption compounds the problem by describing the ordinate as 'normalized to bin size', which is meaningful for the counts in Figures 2 and 3 but not for a mean mass. Please state plainly whether Figure 4 is flat or trends with overdensity, and correct the caption.

Minor objections (11)

[§2.3] The phrase 'third-order-accurate piecewise parabolic monotolic interpolation' contains a typo: 'monotolic' should read 'monotonic'.
[§2.3] The spacetime is written as 'Friedman-Robertson-Walker'; the standard spelling is 'Friedmann-Robertson-Walker'.
[§2.4] The species list in the chemistry description is missing its closing parenthesis and reads '( H, H +,He, He+, He ++, H−, H+2 , H2, and e−.' Please also set the ion notation consistently (H+, He+, He++, H2+, H−, e−) so that the nine species are unambiguous.
[§2.4] The equilibrium cooling model is stated to assume Z = 0.3 Z_sun with no justification for that metallicity and no indication of whether it is a compile-time or run-time choice. A sentence on how a user changes the metallicity, and a citation for the cooling curve itself, would help users.
[§2.2, Eqs. (1)-(2)] The authors state that cosmological terms are omitted from the particle equations of motion 'for simplicity'. Since the code is presented as a cosmology code, it would be worth one sentence pointing the reader to where the comoving-frame equations and the expansion terms are written down (presumably Bryan et al. [8]), so that the omission is not read as an absence.
[§2.2] The gravity description does not state the particle-mesh force softening or the effective force resolution on the finest level. A single sentence on how force resolution relates to the mesh spacing would let users judge whether the code suits a given problem.
[§2.1] The text claims support for 'arbitrary integer ratios of parent and child grid resolution', while Section 3 states that all grids in the test suite are refined by a factor of 2.0. Please clarify whether non-power-of-two refinement ratios are supported and tested, or whether the arbitrary-ratio capability is untested in the runs shown.
[Figure 2 caption] The figure labels as printed ('Enzo Zeus 64dm/64grid', 'Enzo PPM 64dm/128grid', 'Zeus 64dm/64grid High OD') mix code names and prefixes in a way that is not defined anywhere. Please define each label once in the caption, including which runs use PPM versus Zeus hydro and which uses the doubled overdensity threshold.
[§3, paragraph 1] The expression 'Lbox/e = 4096' is undefined; presumably it means L_box divided by the smallest resolvable cell size. Please write it explicitly as L_box/Delta x_min and state the value of Delta x_min in comoving units.
[§2.4] The star formation prescription is described only qualitatively ('gas which is rapidly cooling and increasing in density'), with no parameter values, no statement of the density and cooling-time thresholds, and no caveat about resolution dependence. At minimum, point the reader to where the parameters and their defaults are documented.
[§3, paragraph 1] The sentence 'the total number of cells at the end of the run has increase by a factor of ~8-10' needs the verb corrected to 'has increased', and the range should be given with a consistent notation.

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The paper

The paper claims

Enzo is a publicly released, parallel adaptive-mesh code that concentrates computing power only where cosmic structure forms, coupling dark matter particles to a high-order gas solver.

The reading

The paper introduces Enzo, a three-dimensional, message-passing-parallel cosmology code built on block-structured adaptive mesh refinement. The problem it addresses is one of dynamic range: a galaxy-formation simulation must cover megaparsec scales while resolving structures two or more orders of magnitude smaller, roughly five orders of magnitude in total, which is unaffordable on a single uniform grid. Enzo's answer is to keep a coarse root grid covering the whole volume and to overlay finer rectangular patches only where refinement criteria fire, such as baryon or dark matter overdensity, shocks, the Jeans length, or short cooling times. Dark matter is followed as particles moved by a particle-mesh scheme, gas by a cosmology-modified piecewise parabolic method, and the gravity equation is solved by fast Fourier transform on the periodic root grid and by multigrid relaxation on the subgrids. The paper's supporting evidence is a set of runs showing that the adaptive hierarchy spreads cells across the full density range and improves mean baryon mass resolution by roughly five to ten times over the root grid, with total cell counts growing by about a factor of eight to ten.

What carries the argument

The load-bearing structure is the block-structured adaptive mesh hierarchy of Berger and Colella, in which the root grid carries the periodic cosmological volume and child grids, refined by integer factors of two in these runs, are laid down wherever user-chosen criteria demand. Two solvers sit on this hierarchy and must agree with each other: the elliptic Poisson equation is handled by FFT on the triply periodic root grid and by multigrid relaxation on the non-periodic subgrids, with forces then interpolated to particle positions, while the gas is advanced by a cosmology-modified piecewise parabolic method that solves both the internal energy and total energy equations everywhere so that strong shocks and hypersonic bulk flows keep correct pressures and temperatures. The dual energy formalism is the specific device that lets the code survive cosmological hypersonic flows where kinetic energy dwarfs thermal energy by many orders of magnitude.

Extended reading notes

Core claim

The claim is that a single code can deliver both the large volume and the small-scale resolution that cosmological structure formation demands, without the fixed mass resolution and poor shock handling the authors attribute to smoothed particle hydrodynamics. Enzo achieves this by treating each grid patch as an object in a distributed hierarchy, with a three-zone-deep ghost-zone layer wide enough to feed the hydrodynamics stencil, and by distributing patches across processors with a simple dynamic load-balancing scheme. On top of that skeleton the authors place a full physics set: two radiative cooling models, one assuming collisional equilibrium at a fixed metallicity and one solving a 28-equation primordial reaction network for nine species, several uniform ultraviolet background models after Haardt and Madau, and a heuristic star formation and feedback prescription in which rapidly cooling, densifying gas is converted into star particles that return metals and thermal energy as winds. The quantitative demonstration is that in a $3~h^{-1}$ Mpc box with $64^3$ or $128^3$ root grids and five or six refinement levels, cells populate the entire density range rather than clustering only at high overdensity, and the mean cell mass at the end of a run is about five to ten times smaller than the root-grid mass.

Load-bearing premise

The gravity solver must produce a potential that is consistent across refinement boundaries, since the periodic root grid is handled by a Fourier transform and the subgrids by multigrid relaxation, and the paper states this in a single sentence without an error estimate, a convergence test, or a description of how subgrid boundary values are supplied from the parent grid.

Editorial extensions

If this is right

Cosmological simulations can cover several megaparsecs while resolving kiloparsec-scale structure, which is the range galaxy formation requires.
Low-density gas is well sampled rather than undersampled, unlike particle-based methods, so the Lyman-alpha forest and other underdense regions can be modelled with the same run that resolves collapsed objects.
The same code base serves non-cosmological problems, since the mesh, gravity, and hydro machinery do not depend on the expansion of the universe.
Because the code is released publicly with HDF5 output and MPI portability across IBM SP, SGI Origin, and Linux clusters, results become reproducible and extensible by groups that did not write it.
Adding magnetohydrodynamics and flux-limited radiation diffusion, which the authors say is underway, extends the same hierarchy to magnetized and radiatively driven astrophysical flows.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

The paper never quantifies how accurately the FFT root-grid potential and the multigrid subgrid potential agree at refinement boundaries, so a reader cannot tell from this document whether particle trajectories acquire level-dependent errors; a convergence study comparing a fully refined uniform run against the adaptive run would settle it.
Because the refinement criteria are overdensity, slope, shocks, Jeans length, and cooling time, the effective resolution depends on thresholds the user picks; the authors' own comparison of a doubled overdensity threshold shows the cell count falls while the density distribution barely changes, which suggests the mass-resolution gain is somewhat threshold-insensitive but leaves the accuracy of tha
The star formation prescription is explicitly heuristic, converting rapidly cooling gas into particles that return metals and energy; whether such a sub-grid rule reproduces observed galaxy stellar masses and wind-driven metal enrichment is a separate question the paper does not attempt to answer here.
The stated contrast with smoothed particle hydrodynamics rests on shock resolution and low-density sampling; a direct head-to-head on a problem with a known analytic shock or a known mass function would turn that contrast from a design argument into a measured one.

Original abstract

In this paper we introduce Enzo, a 3D MPI-parallel Eulerian block-structured adaptive mesh refinement cosmology code. Enzo is designed to simulate cosmological structure formation, but can also be used to simulate a wide range of astrophysical situations. Enzo solves dark matter N-body dynamics using the particle-mesh technique. The Poisson equation is solved using a combination of fast fourier transform (on a periodic root grid) and multigrid techniques (on non-periodic subgrids). Euler's equations of hydrodynamics are solved using a modified version of the piecewise parabolic method. Several additional physics packages are implemented in the code, including several varieties of radiative cooling, a metagalactic ultraviolet background, and prescriptions for star formation and feedback. We also show results illustrating properties of the adaptive mesh portion of the code. Enzo is publicly available and can be downloaded at http://cosmos.ucsd.edu/enzo/ .

The compiled record

The paper's own sentences, arranged, kept beside the review and separate from it. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

Compiled by classifier-1.13.0 via TypeSafe API, question bank abstract-p1-20260923, 2026-09-23: 1 request, 6,144 input tokens.

What the abstract itself states, as probabilities: claims first 0.03 · states limitation 0.08 · human participants 0.01 · controlled comparison 0.01 · randomized assignment 0.01 · states quantitative result 0.05 · compares with prior results 0.05 · mentions code or data availability 0.98.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; show every role.

In this paper we introduce Enzo, a 3D MPI-parallel Eulerian block-structured adaptive mesh refinement cosmology code. Enzo is designed to simulate cosmological structure formation, but can also be used to simulate a wide range of astrophysical situations. Enzo solves dark matter N-body dynamics using the particle-mesh technique. The Poisson equation is solved using a combination of fast fourier transform (on a periodic root grid) and multigrid techniques (on non-periodic subgrids). Euler's equations of hydrodynamics are solved using a modified version of the piecewise parabolic method. Several additional physics packages are implemented in the code, including several varieties of radiative cooling, a metagalactic ultraviolet background, and prescriptions for star formation and feedback. We also show results illustrating properties of the adaptive mesh portion of the code. Enzo is publicly available and can be downloaded at http://cosmos.ucsd.edu/enzo/ .

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#	sentence	role	the authors' own work	states the main conclusion	strength
s0	In this paper we introduce Enzo, a 3D MPI-parallel Eulerian block-structured adaptive mesh refinement cosmology code.	contribution 1.00	0.83	0.36	asserted 1.00
s1	Enzo is designed to simulate cosmological structure formation, but can also be used to simulate a wide range of astrophysical situations.	contribution 0.88	0.24	0.10	asserted 0.93
s2	Enzo solves dark matter N-body dynamics using the particle-mesh technique.	method 0.99	0.57	0.04	asserted 1.00
s3	The Poisson equation is solved using a combination of fast fourier transform (on a periodic root grid) and multigrid techniques (on non-periodic subgrids).	method 1.00	0.64	0.03	asserted 1.00
s4	Euler's equations of hydrodynamics are solved using a modified version of the piecewise parabolic method.	method 0.99	0.67	0.03	asserted 1.00
s5	Several additional physics packages are implemented in the code, including several varieties of radiative cooling, a metagalactic ultraviolet background, and prescriptions for star formation and feedback.	method 0.66	0.81	0.04	asserted 1.00
s6	We also show results illustrating properties of the adaptive mesh portion of the code.	result 0.78	0.92	0.06	asserted 1.00
s7	Enzo is publicly available and can be downloaded at http://cosmos.ucsd.edu/enzo/ .	contribution 0.80	0.32	0.04	asserted 1.00

What kind of paper the classifier reports this is: method or tool 1.00 · evidence from simulation or computation 1.00.

What was examined, and what was not

sources read

arXiv listing abstract v1

not examined

full text
figures and tables
references and citing sentences
relations to other papers

levels run

P abstract

not run

S sections
T body sentences
C citations
R cross-paper relations

Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

Figures

**Figure 1.** Real and ghost grids in a hierarchy; real and ghost zones in a grid. Each data field on a real grid is an array of zones with dimensionality equal to that of the simulation (typically 3D in cosmological structure formation). Zones are partitioned into a core block of real zones and a surrounding layer of ghost zones. Real zones are used to store the data field values, and ghost zones are used to temporarily store neighboring grid values when required for updating real zones. The ghost zone layer is three zones deep in order to accomodate the computational stencil in the…

**Figure 2.** Number of cells as a function of baryon overdensity (normalized by bin size) for a representative suite of Enzo cosmology simulations. The simulations are labelled such that the first number corresponds to the number of dark matter particles and the second number shows the root grid size, ie, 64dm/128grid means that the simulation has 643 dark matter particles and a 1283 root grid. Simulations with two different hydrodynamic methods are used. PPM: Piecewise Parabolic Method. [8] Zeus: The hydro method used in the Zeus astrophysical code. [9] algorithm. Several other physics packages

**Figure 3.** Number of cells as a function of baryonic mass (normalized to bin size) for several Enzo simulations with Lbox = 3h −1M pc. The arrows correspond to the mean mass resolution of the root grid for simulation volumes with the same volume but root grids with 643 , 1283 or 2563 cells (labelled N64, N128 and N256, respectively). See

**Figure 4.** Mean baryonic mass in cells as a function of baryon overdensity (normalized to bin size) in Enzo simulations. These are the same simulations (with the same labels) as in

Figures reproduced from arXiv:astro-ph/0403044 by the authors.

References

Works cited (15)

[2]

M. J. Berger and P. Colella. Local adaptive mesh reﬁnement for s hock hydrodynamics. J. Comp. Phys. , 82:64–84, 1989

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[7]

P. R. Woodward and P. Colella. A piecewise parabolic method for gas dynamical simulations. J. Comp. Physics , 54:174, 1984

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[8]

G. L. Bryan, M. L. Norman, J. M. Stone, R. Cen, and J. P. Ostrik er. A piecewise parabolic method for cosmological hydrodynamics. Comp. Phys. Comm. , 89:149–168, 1995

View on Pith 1995
[14]

F. Haardt and P. Madau. Radiative Transfer in a Clumpy Universe . II. The Ultraviolet Extragalactic Background. ApJ, 461:20–+, April 1996

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[15]

R. Cen and J. P. Ostriker. Galaxy formation and physical bias. ApJL, 399:L113–L116, November 1992

View on Pith 1992
[3]

G. L. Bryan and M. L. Norman. A hybrid amr application for cosmolo gy and astrophysics. In N. Chrisochoides, editor, Workshop on Structured Adaptive Mesh Reﬁnement Grid Methods , page 165. IMA Volumes in Mathematics No. 117, 2000

View on Pith 2000
[6]

M. L. Norman and G. L. Bryan. Cosmological adaptive mesh reﬁne ment. In Kohji Tomisaka Shoken M. Miyama and Tomoyuki Hanawa, editors , Numerical Astrophysics : Proceedings of the International Conference on Numerical Astrophysics 1998 (NAP98), held at the National O lympic Memorial Youth Center, Tokyo, Japan, March 10-13, 1998. , page 19. Kluwer Academic, 1999

View on Pith 1998
[1]

J. J. Monaghan. Smoothed particle hydrodynamics. Annual Review of Astronomy & Astrophysics , 30:543, 1992

View on Pith 1992
[4]

G. L. Bryan and M. L. Norman. In D. A. Clarke and M. Fall, editors, Computational Astrophysics; 12th Kingston Meeting on Theo retical As- trophysics, proceedings of meeting held in Halifax; Nova Sc otia; Canada October 17-19; 1996 . ASP Conference Series # 123, 1997

View on Pith 1996
[5]

G. L. Bryan. Fluids in the universe: Adaptive mesh in cosmology. Com- puting in Science and Engineering , 1:2:46, 1999

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[9]

J. M. Stone and M. L. Norman. Zeus-2d: A radiation magnetohyd ro- dynamics code for astrophysical ﬂows in two space dimensions. i - t he hydrodynamic algorithms and tests. ApJ, 80:753, 1992

View on Pith 1992
[10]

J. M. Stone and M. L. Norman. Zeus-2d: A radiation magnetohy dro- dynamics code for astrophysical ﬂows in two space dimensions. ii. th e magnetohydrodynamic algorithms and tests. ApJ, 80:791, 1992

View on Pith 1992
[11]

T. Abel, P. Anninos, Y. Zhang, and M. L. Norman. Modeling primor dial gas in numerical cosmology. New Astronomy , 2:181–207, August 1997

View on Pith 1997
[12]

P. Anninos, Y. Zhang, T. Abel, and M. L. Norman. Cosmological h y- drodynamics with multi-species chemistry and nonequilibrium ionization and cooling. New Astronomy , 2:209–224, August 1997

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[13]

M. Rauch. The Lyman Alpha Forest in the Spectra of QSOs. Annual Review of Astronomy and Astrophysics , 36:267–316, 1998

View on Pith 1998

Forward citations

Cited by 11 Pith papers

Reviewed papers in the Pith corpus that reference this work. Sorted by Pith novelty score. OpenAlex reports about 36 citations worldwide. Full citation record

Smoothed particle magnetohydrodynamics for simulations of galaxy and cosmic structure formation
astro-ph.GA 2026-08 conditional novelty 7.0 of 10

A new conservative SPMHD scheme in SWIFT passes standard tests and achieves the first coupling of the EAGLE galaxy formation model to magnetohydrodynamics.
Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback?
astro-ph.GA 2025-01 conditional novelty 6.0 of 10

Internal Lyman-Werner feedback from a first star inside an atomic-cooling halo reduces accretion onto neighboring protostars and cannot produce a supermassive star, even when molecular hydrogen cooling is artificially...
The evolution of massive black holes and their spins in their galactic hosts
astro-ph.CO 2012-01 conditional novelty 6.0 of 10

Coupling black-hole accretion and mergers to a self-consistent model of galactic gas predicts high black-hole spins at high redshift and low spins near z=0, with the fraction of gas-rich (aligned-spin) mergers declini...
The Baryon Census in a Multiphase Intergalactic Medium: 30% of the Baryons May Still Be Missing
astro-ph.CO 2011-12 conditional novelty 6.0 of 10

Roughly 29% of the universe's baryons remain unaccounted for at low redshift, after revising the O VI-traced warm-hot intergalactic medium upward to about 17% of the total.
Multi-scale initial conditions for cosmological simulations
astro-ph.CO 2011-03 accept novelty 6.0 of 10

Real-space convolution plus an adaptive multigrid Poisson solver produces nested cosmological initial conditions with about 10^-4 relative errors in the refined region, roughly 100 times better than the prior Fourier-...

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Non-linear evolution of f(R) cosmologies I: methodology
astro-ph 2008-07 conditional novelty 6.0 of 10

A multigrid-based N-body method solves the non-linear f(R) scalar field equation and finds roughly 20% enhanced dark matter clustering at fR0 = -1e-5.
Non-linear evolution of f(R) cosmologies II: power spectrum
astro-ph 2008-07 accept novelty 6.0 of 10

First cosmological simulations with the chameleon mechanism show it suppresses f(R) power spectrum enhancements at small scales by up to a factor of four, while leaving measurable signals at intermediate scales.
Cosmological parameters from combining the Lyman-alpha forest with CMB, galaxy clustering and SN constraints
astro-ph 2006-04 accept novelty 6.0 of 10

Adding Lyman-alpha forest power spectra to WMAP3, supernovae and galaxy clustering gives sum of neutrino masses below 0.17 eV at 95 percent confidence, no running of the spectral index, and an effective neutrino numbe...
The Linear Theory Power Spectrum from the Lyman-alpha Forest in the Sloan Digital Sky Survey
astro-ph 2004-07 accept novelty 6.0 of 10

Forward-modeling the SDSS Lyman-alpha forest flux power spectrum through calibrated hydrodynamic simulations yields the linear matter power spectrum amplitude and slope at z=3, with a published chi-squared table for j...
A Multi-Code Analysis Toolkit for Astrophysical Simulation Data
astro-ph.IM 2010-11 accept novelty 5.0 of 10

yt provides a single, code-agnostic, parallel Python toolkit for reading, analyzing, and visualizing adaptive-mesh astrophysical simulation data from Enzo, Orion, RAMSES, FLASH, and Chombo.
The Environmental Impact of Lyman-break Galaxies
astro-ph 2006-03 conditional novelty 5.0 of 10

A cosmological simulation of z=3 galaxies reproduces the 2005 HI flux measurements around Lyman-break galaxies, shows no earlier proximity effect, and underproduces intergalactic CIV and OVI, suggesting smaller early ...

How later papers used it

47 later papers cite it

Evidence: substantial. 31 of the citing papers share no author with it, and 19 of those carry a confident label from Pith's citation classifier.

Pith read 16 of the 56 citing sentences, choosing only those whose citation markers point at this paper alone, and wrote the paraphrases from them. The summary, the counts, the evidence level, the links and the quotes come from code; the summary counts the papers listed below. A later paper is listed under a label when Pith's citation classifier gives one of its sentences that label at probability 0.8 or more (0.95 for support), Pith's reading finds that the citing paper itself did it, and a second check confirms the paraphrase against the sentence. This section lists uses only. It does not list criticism or disagreement, so their absence here says nothing about how the paper has been received. Papers that share an author with this one are listed apart, under "By the same authors". A quote is the citing authors' own sentence, shown when their paper's licence is CC BY, CC BY-SA or CC0. JSON

6 later papers by other authors are listed below: 5 used its method or tool and 1 compared its own results with it. 2 more papers by the same authors are listed: 2 used its method or tool.

Uses its method or tool 7 of 28 papers with this label · 2 by the same authors

Used the cosmological codes GADGET3 and Enzo v2.1.1 with initial conditions that include $v_$ self-consistently.

The impact of the supersonic baryon-dark matter velocity difference on the z~20 21cm background (2012) · 1.00 · paraphrased: the licence does not allow quoting
Carried out all simulations with its modified version of the multi-dimensional hydrodynamics and N-body grid-based code Enzo.

The effect of binding energy and resolution in simulations of the common envelope binary interaction (2017) · 1.00 · paraphrased: the licence does not allow quoting
Used these initial conditions with the cosmological codes GADGET3 and Enzo v2.1.1 with the default piecewise parabolic method to solve the equations of hydrodynamics.

The formation of the first cosmic structures and the physics of the z~20 Universe (2012) · 1.00 · paraphrased: the licence does not allow quoting
Used the publicly available codes, a Lagrangian TreeSPH code and a hybrid adaptive mesh refinement, grid-based code, to run the simulations in this work.

How to Zoom: Bias, Contamination, and Lagrange Volumes in Multimass Cosmological Simulations (2013) · 1.00 · paraphrased: the licence does not allow quoting
Created the initial conditions for the simulations using ENZO, a publicly available cosmological N-body + hydrodynamics code.

The Bispectrum of f(R) Cosmologies (2011) · 1.00 · paraphrased: the licence does not allow quoting

By the same authors

Used the code Enzo to simulate the formation of the first star within a periodic volume 250 comoving kpc on a side.

Accretion onto the First Stellar Mass Black Holes (2008) (same authors) · 1.00 · paraphrased: the licence does not allow quoting
Presented simulations performed with the adaptive mesh refinement code Enzo.

The Formation of Population III Binaries from Cosmological Initial Conditions (2009) (same authors) · 1.00 · paraphrased: the licence does not allow quoting

Compares with it 1 of 2 papers with this label

Compared the result from the identical test, using the pressure-energy formulation without the $∇h$ terms in the EOM, and results from a high-resolution run with Enzo, a grid code.

A General Class of Lagrangian Smoothed Particle Hydrodynamics Methods and Implications for Fluid Mixing Problems (2012) · 0.96 · paraphrased: the licence does not allow quoting

How the literature uses it

45 arXiv papers cite this in 54 sentences

Each citing sentence is taken from the citing paper's LaTeX source and typed by Pith's classifier. A label appears at probability 0.8 or more (0.95 for support), a contest at 0.7 or more; the quoted words are the citing authors'. How each label was checked · JSON

Papers citing it · 16 sentences without a confident label

Uses its method or tool 26 papers

For the data presented in this paper, we solve the ideal MHD equations with self-gravity using the adaptive mesh refinement (AMR) code Enzo [ref] extended to MHD by [ref] .

The Two States of Star Forming Clouds · Numerical Method, Simulations, Analysis · 0.99
Our initial conditions are spherically-averaged halos derived from cosmological initial conditions with the Enzo adaptive mesh refinement (AMR) code [ref] that are photoionized by the star in the ZEUS-MP reactive flow radiative transfer code [ref] .

The Destruction of Cosmological Minihalos by Primordial Supernovae · Introduction · 1.00
In order to study the effects of a global photodissociating background, we take a single “standard” Pop III star formation simulation using the Enzo code [ref] and gradually increase the strength of the Lyman-Werner (H$_2$ photodissociating) background.

Local and Global Radiative Feedback from Population III Star Formation · Effects of a Global Photodissociating Background · 0.99

Uses its data or values 1 paper

< g r a p h i c s > Generating an image from pre-generated set of isodensity surfaces with the isolated galaxy test simulation of [ref] .

AstroBlend: An Astrophysical Visualization Package for Blender · Summary and Future Plans · 0.89

Compares with it 2 papers

We also compare the result from the identical test in , using the pressure-energy formulation but without including the $∇h$ terms in the EOM, as well as the results from a high-resolution run with Enzo [ref] , a grid code.

A General Class of Lagrangian Smoothed Particle Hydrodynamics Methods and Implications for Fluid Mixing Problems · The “Blob” Test · 0.96
The physical properties of the forest obtained from the TreePM/SPH code GADGET-2 are in agreement at the percent level with those inferred from the moving-mesh code AREPO [ref] and with the Eulerian code ENZO [ref] .

IGM Constraints from the SDSS-III/BOSS DR9 Ly-alpha Forest Flux Probability Distribution Function · Hydrodynamical Simulations · 0.82

Cites it as background 4 papers

The parallelization of AMR alogrithms, which should combine the cost/time savings of both methods is not straight forward however and there have been many different approaches [ref] , .

Efficient Parallelization for AMR MHD Multiphysics Calculations; Implementation in AstroBEAR · Introduction · 0.97
Extensive theory has since been developed for the method in different contexts, and mesh refinement algorithms have been widely adopted in the literature [ref] .

Toward a Consistent Framework for High Order Mesh Refinement Schemes in Numerical Relativity · Introduction · 0.92
There are many cosmological hydrodynamic simulation codes available today [ref] .

EUNHA: a new cosmological hydro simulation code · Introduction · 0.94

Discussion

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