From f7ff6bfe1aeb85e96e8b894e0e2a40dc2f7f7a05 Mon Sep 17 00:00:00 2001 From: Lehman Garrison Date: Mon, 23 Jan 2023 16:39:51 -0500 Subject: [PATCH] Update docs theme and citation page --- docs/citation.rst | 76 +++++++++++--------- docs/conf.py | 33 ++++++--- docs/cosmologies.rst | 14 ++-- docs/data-products.rst | 2 +- docs/index.rst | 6 +- docs/nbody-details.rst | 4 +- docs/requirements-dev.txt | 10 --- docs/requirements.txt | 4 +- docs/simulations.rst | 7 +- papers.bib | 148 ++++++++++++++++++++++++++++++-------- 10 files changed, 201 insertions(+), 103 deletions(-) delete mode 100644 docs/requirements-dev.txt diff --git a/docs/citation.rst b/docs/citation.rst index a1f9580e..507a9b89 100644 --- a/docs/citation.rst +++ b/docs/citation.rst @@ -1,37 +1,45 @@ Papers & Citation ================= -Citation --------- -.. TODO: are we asking users to cite all of these papers? Let's be clear. - -Use of AbacusSummit should cite `Maksimova et al. (2021) `_ for the -simulation suite; `Garrison et al. (2021) `_, `Garrison et al. (2019) `_, -and `Garrison et al. (2018) `_ for the Abacus code; -and `Metchnik (2009) `_ -for the initial method. -Applications using the CompaSO halos should cite `Hadzhiyska et al. (2021) `_ for that method; those using the AbacusSummit halo light cone catalogues should cite `Hadzhiyska et al. (2021) `_; and those using the AbacusSummit halo merger trees should cite `Bose et al. `_ -Other citations may be requested as we publish more of the numerical methods. - -We provide a BibTeX file with these references `here `_. - -.. _papers: - -Papers -------- -AbacusSummit is described in `Maksimova et al. (2021, MNRAS, 508, 4017) `_. -The Abacus N-body code is described in `Garrison et al. (2021, MNRAS, 508, 575) `_ and `Garrison et al. (2019, MNRAS, 485, 3370) `_, -where we detail its performance on the `Schneider et al. (2016, JCAP) `_ code -comparison simulation, and in `Garrison et al. (2018, ApJS, 236, -43) `_, -which released an early suite of 125 simulations from 40 -cosmologies (https://lgarrison.github.io/AbacusCosmos/). - -`Garrison et al. (2016, MNRAS, 461, 4125) `_ describes -our initial condition methods. `Hadzhiyska et al. (2021, MNRAS) `_ -describes the CompaSO group finding method. `Hadzhiyska et al. (2021, MNRAS) `_ documents the method for generating light cones on the fly in AbacusSummit; `Bose et al. `_ describes the procedure for generating high-fidelity halo merger trees from AbacusSummit. The AbacusHOD model is presented in `Yuan et al. `_ - -Pinto et al. (in prep) will -describe the Abacus far-field method. Using scale-free simulations, `Joyce et al. (2021, MNRAS, 501, 5051) `_ -describes accuracy tests, and `Garrison et al. (2021, MNRAS, 504, 3550) `_ -validates the force softening scheme. +.. sidebar:: BibTeX References + + .. tip:: + We provide a BibTeX file with the references on this page `here `__. + +Use of AbacusSummit should cite at least the following two papers: + +* *AbacusSummit: a massive set of high-accuracy, high-resolution N-body simulations*, `Maksimova et al. (2021) `__ (describes the simulation suite), and +* *The abacus cosmological N-body code*, `Garrison et al. (2021) `__ (describes the code). + +Users of the AbacusSummit CompaSO halo catalogs (which will be most AbacusSummit users) should additionally cite: + +* *CompaSO: A new halo finder for competitive assignment to spherical overdensities*, `Hadzhiyska et al. (2021) `__ (the CompaSO group finding method) + +Users of the AbacusSummit halo light cone catalogs should cite: + +* *The halo light cone catalogues of AbacusSummit*, `Hadzhiyska et al. (2021) `__ (the generation of halo catalogs on the light cone) + +Users of the AbacusSummit merger trees should cite: + +* *Constructing high-fidelity halo merger trees in abacussummit*, `Bose et al. (2022) `__ (the merger tree method) + +Users of the AbacusHOD module (:doc:`abacusutils:hod`) should cite: + +* *AbacusHOD: a highly efficient extended multitracer HOD framework and its application to BOSS and eBOSS data*, `Yuan et al. (2021) `__ + + +Additional citations of Abacus (which might be used when a work goes beyond just using AbacusSummit data products and is discussing the Abacus code itself) are: + +* *A high-fidelity realization of the Euclid code comparison N-body simulation with ABACUS*, `Garrison et al. (2019) `__ (performance and accuracy of Abacus on the Euclid code comparison simulation, `Schneider et al. (2016) `__) +* *The Abacus Cosmos: A suite of cosmological N-body simulations*, `Garrison et al. (2018) `__ (an early suite of 125 simulations from 40 cosmologies, https://lgarrison.github.io/AbacusCosmos/), +* *Improving initial conditions for cosmological N-body simulations*, `Garrison et al. (2016) `__ (detailing the initial conditions method) +* *A fast N-body scheme for computational cosmology*, `Metchnik (2009) `__ (the inception of the mathematical method for the force solver). + +Other Abacus citations may be requested as we publish more of the numerical methods. + +A related series of papers investigating the accuracy of Abacus and N-body simulations in general using scale-free simulations may be of interest as well: + +* *Accuracy of power spectra in dissipationless cosmological simulations*, `Maleubre et al. (2022) `__ (likewise assesses the accuracy of power spectra) +* *Self-similarity of k-nearest neighbour distributions in scale-free simulations*, `Garrison, Abel, and Eisenstein (2021) `__ +* *Good and proper: self-similarity of N-body simulations with proper force softening*, `Garrison et al. (2021) `__ (validates the force softening scheme using scale-free simulations) +* *Quantifying resolution in cosmological N-body simulations using self-similarity*, `Joyce et al. (2021) `__ (describes accuracy tests using scale-free simulations) \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index ab17e29f..0358304e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -19,8 +19,7 @@ # LHG: this is the author order of the AbacusSummit paper, plus the Phil from the ALCC proposal project = 'AbacusSummit' -copyright = '2021, Nina Maksimova, Lehman Garrison, Daniel Eisenstein, Boryana Hadzhiyska, Sownak Bose, Thomas Satterthwaite, and Philip Pinto' -author = 'Nina Maksimova, Lehman Garrison, Daniel Eisenstein, Boryana Hadzhiyska, Sownak Bose, Thomas Satterthwaite, and Philip Pinto' +copyright = '2023, Nina Maksimova, Lehman Garrison, Daniel Eisenstein, Boryana Hadzhiyska, Sownak Bose, Thomas Satterthwaite, and Philip Pinto' # -- General configuration --------------------------------------------------- @@ -28,7 +27,8 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['readthedocs_ext.readthedocs', 'recommonmark', 'sphinx.ext.intersphinx', 'sphinx.ext.autosectionlabel'] +extensions = ['sphinx.ext.intersphinx', + 'sphinx.ext.autosectionlabel'] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -36,8 +36,8 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - +exclude_patterns = ['_build'] +root_doc = "index" # -- Options for HTML output ------------------------------------------------- @@ -46,17 +46,34 @@ # #html_theme = 'alabaster' #html_theme = 'default' -html_theme = 'sphinx_rtd_theme' +html_theme = 'sphinx_book_theme' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_css_files = ['custom.css'] +html_title = "AbacusSummit" +html_logo = "images/AbacusSummit_logo_bw.png" html_favicon = 'images/icon_red.png' -def setup(app): - app.add_css_file('custom.css') +html_show_sourcelink = False +html_theme_options = { + "repository_url": "https://github.com/abacusorg/AbacusSummit", + "repository_branch": "master", + # "launch_buttons": { + # "binderhub_url": "https://mybinder.org", + # "notebook_interface": "jupyterlab", + # "colab_url": "https://colab.research.google.com/", + # }, + "use_edit_page_button": True, + "use_issues_button": True, + "use_repository_button": True, + "use_download_button": True, + "use_fullscreen_button": False, + "logo_only": True, +} intersphinx_mapping = {'abacusutils': ('https://abacusutils.readthedocs.io/en/latest', None)} diff --git a/docs/cosmologies.rst b/docs/cosmologies.rst index 45f53e8f..e62c5794 100644 --- a/docs/cosmologies.rst +++ b/docs/cosmologies.rst @@ -49,21 +49,23 @@ neutrinos as a smooth component. Cosmologies Table ----------------- -Download the cosmologies table `here `_. -However, in analysis applications, users are encouraged to use the cosmological parameters stored as in the ``header`` field +The following is a listing of all cosmologies used in AbacusSummit simulations. +You can also download the cosmologies table as a CSV `here `__. + +In analysis applications, users are encouraged to use the cosmological parameters stored as in the ``header`` field of the ASDF data product files (which is loaded into the ``meta`` field of Astropy tables, or the ``header`` field of ``CompaSOHaloCatalog`` objects) rather than referencing the cosmologies table. +Another way to access the cosmology of a particular AbacusSummit simulation is +through the ``abacusnbody.metadata`` module: :doc:`abacusutils:metadata` + Column Names The names of the parameter columns in the following table correspond to CLASS parameters. A good place to look for CLASS parameter definitions is this well-commented file: `abacus_base.pre `_. It is derived from the example CLASS input file, so most of the comments are CLASS's. Note that this file is also the base AbacusSummit parameter file used to :ref:`run CLASS`. - For the full CLASS documentation, see `here `_. - - -.. note:: The following table is wide, you may have to scroll to the right to see all the columns. + For the full CLASS documentation, see `here `__. .. csv-table:: :file: ../Cosmologies/cosmologies.csv diff --git a/docs/data-products.rst b/docs/data-products.rst index 22f663c0..cc7dda95 100644 --- a/docs/data-products.rst +++ b/docs/data-products.rst @@ -279,7 +279,7 @@ the inner 90% of the mass relative to this center. [0,30000]. Halo light cone catalogs -~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~ The halo light cone catalogs contain several additional fields listed below. - ``int64_t index_halo``: Index of the halo into the full redshift catalogue diff --git a/docs/index.rst b/docs/index.rst index b90ee4cd..52971ac3 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -2,10 +2,6 @@ sphinx-quickstart on Wed Apr 29 14:38:47 2020. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. - -.. image:: images/AbacusSummit_logo_bw.png - :width: 300px - :align: center AbacusSummit ============ @@ -18,7 +14,7 @@ Computing Facility under a time allocation from the DOE's ALCC program. AbacusSummit was run using the Abacus N-body code. For more information about the code, see :doc:`abacus`. -The specifications of the ~150 simulations that comprise AbacusSumit are given on the :doc:`simulations` page. +The specifications of the 160+ simulations that comprise AbacusSumit are given on the :doc:`simulations` page. The cosmologies used by these simulations are specified on the :doc:`cosmologies` page. diff --git a/docs/nbody-details.rst b/docs/nbody-details.rst index d82b8a0d..716cdefa 100644 --- a/docs/nbody-details.rst +++ b/docs/nbody-details.rst @@ -7,7 +7,7 @@ that affect the accuracy of the outputs (e.g. softening, time stepping, ICs). All of the simulations start at *z* = 99 utilizing second-order Lagrangian Perturbation Theory initial conditions following corrections of first-order particle linear theory; these are described in Garrison -et al. (2016, see :ref:`papers`) and have a target correction redshift of 12. The +et al. (2016, see :doc:`citation`) and have a target correction redshift of 12. The particles are displaced from a cubic grid. The simulations use spline force softening, described in Garrison @@ -24,7 +24,7 @@ by a parameter eta, which is 0.25 in these simulations. Simulations require about 1100 time steps to reach *z* = 0.1. Users of the outputs probably don't need to know much of the numerical -details of the code, but there is one numerical concept that enter +details of the code, but there is one numerical concept that enters into the data products. Abacus uses a cubic grid of size CPD\ :sup:`3`, chosen to tune code speed. For AbacusSummit, CPD is ususally 1701. Processing proceeds in y-z slabs of cells, and particle outputs are diff --git a/docs/requirements-dev.txt b/docs/requirements-dev.txt deleted file mode 100644 index 61afa8b7..00000000 --- a/docs/requirements-dev.txt +++ /dev/null @@ -1,10 +0,0 @@ -Pygments >= 2.3.1 -setuptools >= 41.0.1 -docutils >= 0.14 -mock >= 1.0.1 -pillow >= 5.4.1 -alabaster >= 0.7 -commonmark >= 0.8.1 -recommonmark >= 0.5.0 -sphinx-rtd-theme -readthedocs-sphinx-ext diff --git a/docs/requirements.txt b/docs/requirements.txt index d5f7dd42..ad068530 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,2 +1,2 @@ -sphinx >= 3.0.3 -sphinx-rtd-theme >= 1.0.0rc1 +sphinx >= 4.2 +sphinx_book_theme >= 0.3 diff --git a/docs/simulations.rst b/docs/simulations.rst index b60aba34..09415984 100644 --- a/docs/simulations.rst +++ b/docs/simulations.rst @@ -73,14 +73,13 @@ and ph4999 will be irregular. Simulations Table ----------------- -Download the simulations table `here `_. +The following is a complete listing of the AbacusSummit simulations. +You can also download this table as a CSV file `here `_. -The cosmologies in the "Cosm" column are tabulated in :doc:`cosmologies`. +The numbers in the "Cosm" column correspond to cosmologies in the :ref:`cosmologies:Cosmologies Table`. The "PPD" column is the number of particles-per-dimension. -.. note:: The following table is wide, you may have to scroll to the right to see all the columns. - .. csv-table:: :file: ../Simulations/simulations.csv :header-rows: 1 diff --git a/papers.bib b/papers.bib index 240c3e7a..a73e5b9f 100644 --- a/papers.bib +++ b/papers.bib @@ -1,3 +1,20 @@ +@ARTICLE{10.1093/mnras/stab2484, + author = {Maksimova, Nina A and Garrison, Lehman H and Eisenstein, Daniel J and Hadzhiyska, Boryana and Bose, Sownak and Satterthwaite, Thomas P}, + title = "{AbacusSummit: a massive set of high-accuracy, high-resolution N-body simulations}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {508}, + number = {3}, + pages = {4017-4037}, + year = {2021}, + month = {09}, + abstract = "{We present the public data release of the AbacusSummit cosmological N-body simulation suite, produced with the Abacus N-body code on the Summit supercomputer of the Oak Ridge Leadership Computing Facility. Abacus achieves \\$\\mathcal \\{O\\}(10^\\{-5\\})\\$ median fractional force error at superlative speeds, calculating 70M particle updates per second per node at early times, and 45M particle updates per second per node at late times. The simulation suite totals roughly 60 trillion particles, the core of which is a set of 139 simulations with particle mass \\$2\\times 10^\\{9\\}\\, h^\\{-1\\}\\, \\mathrm\\{M\\}\_\\odot\\$ in box size \\$2\\, h^\\{-1\\}\\, \\mathrm\\{Gpc\\}\\$. The suite spans 97 cosmological models, including Planck 2018, previous flagship simulation cosmologies, and a linear derivative and cosmic emulator grid. A subsuite of 1883 boxes of size \\$500\\, h^\\{-1\\}\\, \\mathrm\\{Mpc\\}\\$ is available for covariance estimation. AbacusSummit data products span 33 epochs from z = 8 to 0.1 and include light cones, full particle snapshots, halo catalogues, and particle subsets sampled consistently across redshift. AbacusSummit is the largest high-accuracy cosmological N-body data set produced to date.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stab2484}, + url = {https://doi.org/10.1093/mnras/stab2484}, + eprint = {https://academic.oup.com/mnras/article-pdf/508/3/4017/40811763/stab2484.pdf}, +} + + @ARTICLE{10.1093/mnras/stab2482, author = {Garrison, Lehman H and Eisenstein, Daniel J and Ferrer, Douglas and Maksimova, Nina A and Pinto, Philip A}, title = "{The abacus cosmological N-body code}", @@ -14,21 +31,6 @@ @ARTICLE{10.1093/mnras/stab2482 eprint = {https://academic.oup.com/mnras/article-pdf/508/1/575/40458823/stab2482.pdf}, } -@ARTICLE{10.1093/mnras/stab2484, - author = {Maksimova, Nina A and Garrison, Lehman H and Eisenstein, Daniel J and Hadzhiyska, Boryana and Bose, Sownak and Satterthwaite, Thomas P}, - title = "{AbacusSummit: a massive set of high-accuracy, high-resolution N-body simulations}", - journal = {Monthly Notices of the Royal Astronomical Society}, - volume = {508}, - number = {3}, - pages = {4017-4037}, - year = {2021}, - month = {09}, - abstract = "{We present the public data release of the AbacusSummit cosmological N-body simulation suite, produced with the Abacus N-body code on the Summit supercomputer of the Oak Ridge Leadership Computing Facility. Abacus achieves \\$\\mathcal \\{O\\}(10^\\{-5\\})\\$ median fractional force error at superlative speeds, calculating 70M particle updates per second per node at early times, and 45M particle updates per second per node at late times. The simulation suite totals roughly 60 trillion particles, the core of which is a set of 139 simulations with particle mass \\$2\\times 10^\\{9\\}\\, h^\\{-1\\}\\, \\mathrm\\{M\\}\_\\odot\\$ in box size \\$2\\, h^\\{-1\\}\\, \\mathrm\\{Gpc\\}\\$. The suite spans 97 cosmological models, including Planck 2018, previous flagship simulation cosmologies, and a linear derivative and cosmic emulator grid. A subsuite of 1883 boxes of size \\$500\\, h^\\{-1\\}\\, \\mathrm\\{Mpc\\}\\$ is available for covariance estimation. AbacusSummit data products span 33 epochs from z = 8 to 0.1 and include light cones, full particle snapshots, halo catalogues, and particle subsets sampled consistently across redshift. AbacusSummit is the largest high-accuracy cosmological N-body data set produced to date.}", - issn = {0035-8711}, - doi = {10.1093/mnras/stab2484}, - url = {https://doi.org/10.1093/mnras/stab2484}, - eprint = {https://academic.oup.com/mnras/article-pdf/508/3/4017/40811763/stab2484.pdf}, -} @ARTICLE{10.1093/mnras/stab2980, author = {Hadzhiyska, Boryana and Eisenstein, Daniel and Bose, Sownak and Garrison, Lehman H and Maksimova, Nina}, @@ -60,24 +62,40 @@ @ARTICLE{10.1093/mnras/stab3066 } -@misc{bose2021constructing, - title={Constructing high-fidelity halo merger trees in AbacusSummit}, - author={Sownak Bose and Daniel J. Eisenstein and Boryana Hadzhiyska and Lehman H. Garrison and Sihan Yuan}, - year={2021}, - eprint={2110.11409}, - archivePrefix={arXiv}, - primaryClass={astro-ph.CO} - } - -@misc{yuan2021abacushod, - title={AbacusHOD: A highly efficient extended multi-tracer HOD framework and its application to BOSS and eBOSS data}, - author={Sihan Yuan and Lehman H. Garrison and Boryana Hadzhiyska and Sownak Bose and Daniel J. Eisenstein}, - year={2021}, - eprint={2110.11412}, - archivePrefix={arXiv}, - primaryClass={astro-ph.CO} +@article{10.1093/mnras/stac555, + author = {Bose, Sownak and Eisenstein, Daniel J and Hadzhiyska, Boryana and Garrison, Lehman H and Yuan, Sihan}, + title = "{Constructing high-fidelity halo merger trees in abacussummit}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {512}, + number = {1}, + pages = {837-854}, + year = {2022}, + month = {03}, + abstract = "{Tracking the formation and evolution of dark matter haloes is a critical aspect of any analysis of cosmological N-body simulations. In particular, the mass assembly of a halo and its progenitors, encapsulated in the form of its merger tree, serves as a fundamental input for constructing semi-analytic models of galaxy formation and, more generally, for building mock catalogues that emulate galaxy surveys. We present an algorithm for constructing halo merger trees from abacussummit, the largest suite of cosmological N-body simulations performed to date consisting of nearly 60 trillion particles, and which has been designed to meet the Cosmological Simulation Requirements of the Dark Energy Spectroscopic Instrument (DESI) survey. Our method tracks the cores of haloes to determine associations between objects across multiple time slices, yielding lists of halo progenitors and descendants for the several tens of billions of haloes identified across the entire suite. We present an application of these merger trees as a means to enhance the fidelity of abacussummit halo catalogues by flagging and ‘merging’ haloes deemed to exhibit non-monotonic past merger histories. We show that this cleaning technique identifies portions of the halo population that have been deblended due to choices made by the halo finder, but which could have feasibly been part of larger aggregate systems. We demonstrate that by cleaning halo catalogues in this post-processing step, we remove potentially unphysical features in the default halo catalogues, leaving behind a more robust halo population that can be used to create highly accurate mock galaxy realizations from abacussummit.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stac555}, + url = {https://doi.org/10.1093/mnras/stac555}, + eprint = {https://academic.oup.com/mnras/article-pdf/512/1/837/42996773/stac555.pdf}, } + +@article{10.1093/mnras/stab3355, + author = {Yuan, Sihan and Garrison, Lehman H and Hadzhiyska, Boryana and Bose, Sownak and Eisenstein, Daniel J}, + title = "{AbacusHOD: a highly efficient extended multitracer HOD framework and its application to BOSS and eBOSS data}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {510}, + number = {3}, + pages = {3301-3320}, + year = {2021}, + month = {11}, + abstract = "{We introduce the AbacusHOD model and present two applications of AbacusHOD and the AbacusSummit simulations to observations. AbacusHOD is a Halo Occupation Distribution (HOD) framework written in Python that is particle-based, multitracer, highly generalized, and highly efficient. It is designed specifically with multitracer/cosmology analyses for next-generation large-scale structure surveys in mind, and takes advantage of the volume and precision offered by the new state-of-the-art AbacusSummit cosmological simulations. The model is also highly customizable and should be broadly applicable to any upcoming surveys and a diverse range of cosmological analyses. In this paper, we demonstrate the capabilities of the AbacusHOD framework through two example applications. The first example demonstrates the high efficiency and the large HOD extension feature set through an analysis of full-shape redshift-space clustering of BOSS galaxies at intermediate to small scales (\\$\\lt 30\\, h^\\{-1\\}\\$ Mpc), assessing the necessity of introducing secondary galaxy biases (assembly bias). We find strong evidence for using halo environment instead of concentration to trace secondary galaxy bias, a result which also leads to a moderate reduction in the ‘lensing is low’ tension. The second example demonstrates the multitracer capabilities of the AbacusHOD package through an analysis of the extended Baryon Oscillation Spectroscopic Survey cross-correlation measurements between three different galaxy tracers: luminous red galaxies, emission-line galaxies, and quasi-stellar objects. We expect the AbacusHOD framework, in combination with the AbacusSummit simulation suite, to play an important role in a simulation-based analysis of the upcoming Dark Energy Spectroscopic Instrument data sets.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stab3355}, + url = {https://doi.org/10.1093/mnras/stab3355}, + eprint = {https://academic.oup.com/mnras/article-pdf/510/3/3301/42147651/stab3355.pdf}, +} + + @ARTICLE{2019MNRAS.485.3370G, author = {{Garrison}, Lehman H. and {Eisenstein}, Daniel J. and {Pinto}, Philip A.}, title = "{A high-fidelity realization of the Euclid code comparison N-body simulation with ABACUS}", @@ -116,6 +134,7 @@ @ARTICLE{2018ApJS..236...43G adsnote = {Provided by the SAO/NASA Astrophysics Data System} } + @ARTICLE{2016MNRAS.461.4125G, author = {{Garrison}, Lehman H. and {Eisenstein}, Daniel J. and {Ferrer}, Douglas and {Metchnik}, Marc V. and {Pinto}, Philip A.}, @@ -135,6 +154,7 @@ @ARTICLE{2016MNRAS.461.4125G adsnote = {Provided by the SAO/NASA Astrophysics Data System} } + @PHDTHESIS{2009PhDT.......175M, author = {{Metchnik}, Marc Victor Leonard}, title = "{A fast N-body scheme for computational cosmology}", @@ -146,3 +166,69 @@ @PHDTHESIS{2009PhDT.......175M } +@article{10.1093/mnras/staa3434, + author = {Joyce, Michael and Garrison, Lehman and Eisenstein, Daniel}, + title = "{Quantifying resolution in cosmological N-body simulations using self-similarity}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {501}, + number = {4}, + pages = {5051-5063}, + year = {2020}, + month = {11}, + abstract = "{We demonstrate that testing for self-similarity in scale-free simulations provides an excellent tool to quantify the resolution at small scales of cosmological N-body simulations. Analysing two-point correlation functions measured in simulations using abacus , we show how observed deviations from self-similarity reveal the range of time and distance scales in which convergence is obtained. While the well-converged scales show accuracy below 1 per cent, our results show that, with a small force softening length, the spatial resolution is essentially determined by the mass resolution. At later times, the lower cut-off scale on convergence evolves in comoving units as a−1/2 (a being the scale factor), consistent with a hypothesis that it is set by two-body collisionality. A corollary of our results is that N-body simulations, particularly at high red-shift, contain a significant spatial range in which clustering appears converged with respect to the time-stepping and force softening but has not actually converged to the physical continuum result. The method developed can be applied to determine the resolution of any clustering statistic and extended to infer resolution limits for non-scale-free simulations.}", + issn = {0035-8711}, + doi = {10.1093/mnras/staa3434}, + url = {https://doi.org/10.1093/mnras/staa3434}, + eprint = {https://academic.oup.com/mnras/article-pdf/501/4/5051/35926462/staa3434.pdf}, +} + + +@article{10.1093/mnras/stab1096, + author = {Garrison, Lehman H and Joyce, Michael and Eisenstein, Daniel J}, + title = "{Good and proper: self-similarity of N-body simulations with proper force softening}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {504}, + number = {3}, + pages = {3550-3560}, + year = {2021}, + month = {04}, + abstract = "{Analysis of self-similarity in scale-free N-body simulations reveals the spatial and temporal scales for which statistics measured in cosmological simulations are converged to the physical continuum limit. We examine how the range of scales in which the two-point correlation function is converged depends on the force softening length and whether it is held constant in comoving or proper coordinates. We find that a proper softening that reaches roughly 1/30th of the inter-particle spacing by the end of the simulation resolves the same spatial and temporal scales as a comoving softening of the same length while using a third fewer time-steps, for a range of scale factors typical to Lambda cold dark matter (ΛCDM) simulations. We additionally infer an inherent resolution limit, set by the particle mass and scaling as a−1/2, beyond which reducing the softening does not improve the resolution. We postulate a mapping of these results with spectral index n = −2 to ΛCDM simulations.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stab1096}, + url = {https://doi.org/10.1093/mnras/stab1096}, + eprint = {https://academic.oup.com/mnras/article-pdf/504/3/3550/37888807/stab1096.pdf}, +} + + +@article{10.1093/mnras/stac578, + author = {Maleubre, Sara and Eisenstein, Daniel and Garrison, Lehman H and Joyce, Michael}, + title = "{Accuracy of power spectra in dissipationless cosmological simulations}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {512}, + number = {2}, + pages = {1829-1842}, + year = {2022}, + month = {03}, + abstract = "{We exploit a suite of large N-body simulations (up to N = 40963) performed with abacus, of scale-free models with a range of spectral indices n, to better understand and quantify convergence of the matter power spectrum. Using self-similarity to identify converged regions, we show that the maximal wavenumber resolved at a given level of accuracy increases monotonically as a function of time. At 1 per cent level it starts at early times from a fraction of \\$k\_\\Lambda\\$, the Nyquist wavenumber of the initial grid, and reaches at most, if the force softening is sufficiently small, \\$\\{\\sim\\}2\\{-\\}3 k\_\\Lambda\\$ at the very latest times we evolve to. At the \\$5\\{\\{\\ \\rm per\\ cent\\}\\}\\$ level, accuracy extends up to wavenumbers of order \\$5k\_\\Lambda\\$ at late times. Expressed as a suitable function of the scale-factor, accuracy shows a very simple n-dependence, allowing a extrapolation to place conservative bounds on the accuracy of N-body simulations of non-scale-free models like LCDM. We note that deviations due to discretization in the converged range are not well modelled by shot noise, and subtracting it in fact degrades accuracy. Quantitatively our findings are broadly in line with the conservative assumptions about resolution adopted by recent studies using large cosmological simulations (e.g. Euclid Flagship) aiming to constrain the mildly non-linear regime. On the other hand, we remark that conclusions about small-scale clustering (e.g. concerning the validity of stable clustering) obtained using PS data at wavenumbers larger than a few \\$k\_\\Lambda\\$ may need revision in light of our convergence analysis.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stac578}, + url = {https://doi.org/10.1093/mnras/stac578}, + eprint = {https://academic.oup.com/mnras/article-pdf/512/2/1829/43026623/stac578.pdf}, +} + + +@article{10.1093/mnras/stab3160, + author = {Garrison, Lehman H and Abel, Tom and Eisenstein, Daniel J}, + title = "{Self-similarity of k-nearest neighbour distributions in scale-free simulations}", + journal = {Monthly Notices of the Royal Astronomical Society}, + volume = {509}, + number = {2}, + pages = {2281-2288}, + year = {2021}, + month = {10}, + abstract = "{We use the k-nearest neighbour probability distribution function (kNN-PDF; Banerjee \\& Abel 2021a) to assess convergence in a scale-free N-body simulation. Compared to our previous two-point analysis, the kNN-PDF allows us to quantify our results in the language of haloes and numbers of particles, while also incorporating non-Gaussian information. We find good convergence for 32 particles and greater at densities typical of haloes, while 16 particles and fewer appear unconverged. Halving the softening length extends convergence to higher densities, but not to fewer particles. Our analysis is less sensitive to voids, but we analyse a limited range of underdensities and find evidence for convergence at 16 particles and greater even in sparse voids.}", + issn = {0035-8711}, + doi = {10.1093/mnras/stab3160}, + url = {https://doi.org/10.1093/mnras/stab3160}, + eprint = {https://academic.oup.com/mnras/article-pdf/509/2/2281/41199811/stab3160.pdf}, +}