fleshed out the introductory sections

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "importer"]
+	path = importer
+	url = ssh://git@git.kluster.moll.re:2222/remoll/typst-notebook-cell-importer

abstract.typ

@@ -1,3 +1,4 @@
+#import "helpers.typ": *
 = Abstract
-We present refinements to the BEoRN framework, a semi-numerical simulation suite that generates 21-cm maps of the cosmic dawn and the epoch of reionization. The refinements include a self-consistent treatment of the evolution of individual sources, which allows for a more accurate prediction of the 21-cm signal.
+We present an updated version of the #beorn framework, a semi-numerical simulation suite that generates maps of the cosmic dawn and the epoch of reionization. The refinements include a self-consistent treatment of the evolution of individual galaxies, a parametrization of stochasticity of the mass accretion rate, and a general optimization that allows for speedier simulation runs.
-We validate the refined suite against ?? and quantify the gain in consistency resulting from the more accurate treatment of the sources.
+We validate the improved version of the suite against ??. We employ the Thesan-Dark simulation to inder halo mass history and demonstrate the effect of this more detailed treatment.

conclusion.typ

@@ -1,2 +1,14 @@
-= Conclusion
+#import "importer/main.typ": *
-#lorem(900)
+#import "helpers.typ": *
+
+= Conclusion <conclusion>
+
+Upcoming refinements:
+
+- implement merger tree growth fitting based on a more sophisiticated growth model (e.g. based on the PS formalism)
+-
+
+- The sensitivity of the results to the growth rate suggest that more refined halo finding and growth tracking algorithms should be investigated
+Where is rockstar?
+
+

halo_mass_history.typ

@@ -1 +1,121 @@
-= Halo mass history
+#import "importer/main.typ": *
+#import "helpers.typ": *
+
+= Halo mass history <halo_mass_history>
+
+This section delves into the central role of the halo mass evolution for the results of the simulation.
+
+== Modelling mass accretion
+
+Generalized mass accretion rate and its simplification in the exponential growth model.
+
+As described in @hmreio the fundamental assumption of #beorn is the halo model of reionization by @schneider2023cosmologicalforecast21cmpower.
+// no need to recite?
+It describes how observables of reionization can be parametrized in terms of the halo mass and more specifically its rate of change since they are derived from the star formation rate expressed in @eq:star_formation_rate.
+In this simplified model, for a given star formation efficiency
+#footnote[
+  Note that the assumption of a fixed star formation efficiency or even an analytic expression as a function of halo mass is a simplification.
+  // Citation
+  The investigation of stochasticity has been subject to separate research (e.g. "missing").
+],
+the halo mass history is the single most impactful property besides the mass itself.
+
+
+// . In particular we express the star formation rate $dot(M)_star$ through the star formation efficiency $f_star$ and the halo mass $M_"h"$ as follows:
+// $
+//   dot(M)_star = f_star (M_h) dot dot(M_h)
+// $
+
+#beorn's goal is to provide simulations of the map-level contributions to the $21 "cm"$ signal, meaning that we can not rely on a distribution of halo masses and accretion rates alone. Instead #beorn leverages large scale N-body simulations to provide a spatial distribution of halos. In its introduction #cite(<Schaeffer_2023>, form: "normal") #beorn used the PkdGrav3 suite as a generator of the halo distribution. Halo growth was then modelled through an exponential growth model
+$
+  M_"h" (z) = M_"h" (z_0) dot exp[-alpha (z - z_0)]
+$
+where $alpha = - dot(M_"h") / M_"h"$ is a free parameter describing the specific mass accretion rate. Following `@???` a value of $alpha = 0.79$ was used as a fiducial value for all halos, independent of their mass or redshift.
+
+In the following we will motivate the need for a more precise treatment of the halo mass history and show how we can leverage the data provided by the THESAN simulation suite to obtain a more precise model.
+
+// In a purely formal investigation where a qualitative prediction is derived from a well-defined halo mass distribution, the mass history is simply obtained as a direct derivation from the mass distribution. The simulations made by #beorn aim to provide 3D data that allows for quantitative conclusions. To this end a spatial distribution of the halo mass history is required, as provided by large scale simulations
+// #footnote[
+//   As described previously the halo model allows us to restrict the simulation to dark matter only, allowing for a more efficient simulation of the large scale structure.
+// ]
+// // Cite pkdgrav, Illustris, THESAN
+// .
+
+
+== Effect on radiation profiles
+#let notebook = json("../workdir/11_visualization/alpha_dependence_of_profiles.ipynb")
+
+In order to illustrate the necessity of a refined mass history model, we first investigate the effect of different mass accretion rates on the resulting radiation profiles. To this end we consider halos at fixed masses and vary their accretion rates around the fiducial value of $alpha = 0.79$.
+
+
+@Kannan_2021 also shows that reionization history is different for different gas densitites, i.e. halo masses. We also show from a profile perspective that treating halo accretion as a free parameter can lead to significant differences in the resulting profiles.
+
+
+== The THESAN simulation
+
+In order to generate precise map-level predictions of the 21cm signal, #beorn combines the halo model of reionization with large scale N-body simulations which provide realistic snapshots of the dark matter distribution.  They constitute the fundamental input to the halo model amd give a spatial context to the generated profiles.
+
+Past iterations @Schaeffer_2023 #beorn have used different
+#cite(<Schaeffer_2023>, form: "normal")
+means to generate these snapshots, including the 21cmfast emulator as a validation and the PkdGrav3 N-body code as a large signal generator.
+
+For the purposes of this thesis we don't aim to run the largest possible simulation, but rather to refine the underlying model. To this end, we use the publicly available data from the THESAN simulation suite
+#cite(<Kannan_2021>, form: "normal")
+#cite(<Garaldi_2022>, form: "normal")
+#cite(<Smith_2022>, form: "normal")
+. The #smallcaps[Thesan-Dark] simulation in particular provides a dark matter only simulation and provides halo catalogs and merger trees.
+
+With a box length of $95.5 "cMpc"$ it provides a sufficient volume to avoid box size effects
+// CITATION
+while still allowing us to refine the underlying model without excessive computational cost. The simulation has two variants with different mass resolutions:
+... // TODO
+which allow us to perform convergence tests as described in @validation.
+
+
+
+// The simulation has two main limitations: First, the mass resolution of $3.12 * 10^7 "M_⊙"$ means that halos below a mass of $10^9 "M_⊙"$ are not resolved. This is particularly relevant as these low mass halos are expected to contribute significantly to the ionizing photon budget at high redshifts #cite(<Kannan_2021>, form: "normal"). To account for this, we use boosted models of star formation efficiency as described in section <sf_efficiency>. Second, the simulation only provides snapshots down to a redshift of $z=5.5$. As reionization is expected to be completed by this time, this does not impact our results.
+
+Thesan halo catalog and the motivation to increase the cutoff.
+
+At the same time THESAN low mass halos seem overabundant which is why we use boosted models of star formation efficiency.
+
+
+
+
+@Kannan_2021 describes the nuance of using thesan 1 vs thesan 2 for the halo mass:
+the lowest mass halos which are not resolved by thesan 2 form small bubbles quickly and as early as z=10 and contribute to the ionization budget at early times
+
+
+
+=== Merger trees
+#let notebook = json("../workdir/11_visualization/show_trees.ipynb")
+
+The central representation of halo mass evolution is given by merger trees. These tree-like structures describe the halo history in terms of the mergers of its smaller progenitors. A merger tree is constructed by linking halos in consecutive snapshots of the simulation where each halo as a single descendant but potentially multiple progenitors. As described in ... THESAN
+
+The main progenitor can be used as a tracer of the halo mass history if we assume that the halo mass growth is dominated by mergers.
+// Has this been shown to be true somewhere?
+Beyond that, the main progenitor will be the main contributor in terms of stellar mass which is the main quantity of interest for the reionization model. Utilizing the trees provided by
+
+#figure(
+  image_cell(notebook, cell_id: "merger_tree_and_fitting"),
+  caption: "Example of a merger tree and the fitting of its main progenitor's mass history.",
+
+) <fig:merger_tree_and_fitting>
+
+
+- How we treat incomplete trees
+- how we treat invalid trees
+
+
+
+== Resulting distribution
+#let notebook = json("../workdir/11_visualization/evolution_of_alphas.ipynb")
+
+
+#figure(
+  image_cell(notebook, cell_id: "alpha_evolution_vs_redshift"),
+  caption: "??",
+
+
+) <fig:alpha_evolution_vs_redshift>
+

helpers.typ

@@ -0,0 +1,2 @@
+// write the beorn name in a monospace font
+#let beorn = raw("BEoRN")

implementation.typ

@@ -1,11 +1,26 @@
-= Implementation of changes
+#import "helpers.typ": *
+
+= Implementation of changes <implementation>
 
 This section describes the changes and improvements that were necessary to adapt the simulation suite in order to achieve the refined procedure. We distinguish between necessary changes that were required to reflect the underlying model and "beneficial" changes that only indirectly affect the quality of the simulation outputs.
 
-== Necessary changes
+== Profile generation for extended parameter spce
+- vectorized computation of profiles
+- caching of profiles
+
+== Parallel binned painting
+- shared memory multiprocessing
+- excess handling from overlaps
+
+== Merger tree processing
 Fundamental changes include:
 -
 
 
 == Secondary changes
-Beorn was very opinionated in its assumptions and initial data. Since we intend it to create fast and reusable realisations we adapted the code to be more easily adjustable.
+#beorn was very opinionated in its assumptions and initial data. Since we intend it to create fast and reusable realisations we adapted the code to be more easily adjustable.
+- better io
+- better loading
+- refactoring for modularity
+- refined outputs for testing + validation
+

introduction.typ

@@ -1,160 +1,194 @@
+#import "helpers.typ": *
 = Introduction
 
-The earliest cosmological events (such as the formation of the first astrophysical objects - stars, galaxies, black holes...) have a profound influence on the evolution of the universe. Though poorly understood, these events have shaped the characteristics of our current uninverse, including the structure and distribution of matter itself.
+The earliest cosmological events (such as the formation of the first astrophysical objects - stars, galaxies, black holes...) have a profound influence on the evolution of the universe. Though poorly understood, these events have shaped the characteristics of our current universe, including the structure and distribution of matter itself.
 // Citation about an overview paper on ionization vs structure formation.
 Despite the milestones achieved in observational cosmology
 // Citation about CMB measurements, JWST, etc.
 , many aspects of the early universe and its dark ages remain difficult to probe. While traditional measurements provide insights into relatively recent epochs, and the cosmic microwave background (CMB) serves as an early snapshot of the universe, the dark ages are incompatible with direct observations. They represent the critical link between the late-time universe and the primordial conditions.
+// This period is crucial as it sets the stage for the subsequent evolution of the universe, including the formation of galaxies and large-scale structures.
 
-The dark ages of the universe refer to the period after recombination where the primordial atoms remain neutral. They are characterized by a total lack of sources of radiation (beyond the radiation background).
+The epoch of reionization (EOR) spans the period from the end of the dark ages to the universe becoming fully ionized again. It simultaneously is affected by the fundamental mechanisms
-The dominant interactions during that period are either gravitational or due to the cooling of the primordial gas. The formation of the first stars, called population III stars
+// reformulate
+and also affects the subsequent evolution of the universe.
+
+$=>$ reionization can serve as a constraint on cosmological models.
+// Paper by aurel on that
+
+Understanding and being able to model the EOR is therefore crucial for a comprehensive picture of cosmology.
+
+The dark ages of the universe refer to the period after recombination where the primordial atoms remain neutral. They are characterized by the total lack of sources of radiation (beyond the radiation background). The dominant interactions during that period are either gravitational or due to the cooling of the primordial gas. The formation of the first stars is obstructed by the lack of efficient cooling mechanisms in the absence of heavier nuclei. With the simplest cooling channel being the deexcitation of atomic hydrogen, the gas inside a virialized structure can only collapse if the enclosed mass is high enough. This so called atomic cooling limit sets a minimum mass for the halos that can host star formation at around $10^8 M_(dot.circle)$.
+
+molecular cooling as a "workaround"
+but molecular hydrogen is destroyed by radiation from stars
+=> argument that there is no "galaxy" in that sense below
+
+The end of the dark ages is marked by the formation of the first generation of stars, called population III stars
 // Citation about Pop III stars and their role in the cosmic dawn.
-, marks the beginning of the cosmic dawn and with it the process of reionization.
+which...
-
+During the cosmic dawn ...
-....
 
 
 
 The large amounts of neutral hydrogen in the intergalactic medium (IGM) during the dark ages and cosmic dawn allow for an additional mode of observation: the 21-cm line emission. Due to the hyperfine transition of neutral hydrogen
-// This period is crucial as it sets the stage for the subsequent evolution of the universe, including the formation of galaxies and large-scale structures.
 
 
-Paragraph about the earliest cosmlogical events, leading up to the central importance of reionization.
 
-Points to mention
+The main purpose of simulations is to constrain EOR observables, in particular the 21-cm signal.
-- pop III stars and cosmic dawn
+// Keep the below?
+Combined with upcoming observations from ... these simulations will generate a wealth of information about the early universe, at a range of redshifts that has previously been inaccessible. With the highest sensitivity and resolution forecasted for these observations, the simulations must be able to capture the full dynamic range of the interactions, from the small scale physics of star formation and feedback to the large scale structure of the universe.
+
+State of the art simulations need to implement a range of physical processes, including gravitational interactions, hydrodynamics, radiative transfer, and feedback mechanisms. Prominent examples include the THESAN simulations
+#cite(<Kannan_2021>, form: "normal")
+#cite(<Garaldi_2022>, form: "normal")
+#cite(<Smith_2022>, form: "normal")
+and ... .
+Another approach is to use ray-tracing algorithms which give detailed descriptions of the radiative transfer.
+// C2ray?
+These methods are computationally expensive which limits their applicability for large scale simulations.
+
+// Shortcomings of similar codes (as noted in #beorn paper). => justification for the development of #beorn (@Schaeffer_2023).
+
+This work presents #beorn, the Bubbles during the _Epoch of Reionization Numerical simulator_ by @Schaeffer_2023, and the refinements we make to achieve self-consistency. In its simplest description #beorn is the implementation of the "halo model of reionization" by @schneider2023cosmologicalforecast21cmpower. In this model the radiative interactions are treated as spherically symmetric around a halo-scale source. This effectively reduces the dimensionality of the radiative transfer problem. #beorn uses the 1-d profiles generated by this model to paint the 3-d space around sources which are obtained from a large scale N-body simulation. A distinguishing feature of #beorn is the self-consistent treatment of the growth of individual sources over the course of the simulation. The first iteration of #beorn focused on the effect of emitted photons whereas this work focuses on the effects of gravitational mass accretion. We show that the radiation profiles are sensitive to the growth rate of the sources and that an accurate treatment of the source growth has an impact on the resulting 21-cm signal.
+// Mention that this is treated in more detail in @procedure
+
+This report is structured as follows: @procedure describes the details of the simulation procedure, including the underlying model. @halo_mass_history explains how mass evolution is modelled and its impact on the profiles.
+// not any profiles.
+In @implementation we give an overview of the implementation of the self-consistent treatment of mass accretion. In @validation we validate the refined procedure and in @results we compare the resulting signal to quantify the impact of mass accretion. @conclusion summarizes the findings and discusses potential future improvements.
+
+
+
+
+Other points to mention
 - wouthuysen
 - cold reionization
 
-Mention of recent observational advancements that highlight the relevance of larger + more precise simulations that capture the full dynamic range of the interactions.
 
-Shortcomings of similar codes (as noted in beorn paper).
+how #beorn compares to traditional approaches
-
-Assumptions made by beorn and what inaccuracies they introduce.
-e.g. papers like "2309...." suggest a revised halo mass growth.
-e.g. bursty star formation as presented by Romain Teyssier
-
-Refer to the "halo model of reionization" 2302
 
 
-The hyperfine transition of neutral hydrogen generates photons at
+
-the wavelength of 21 cm, opening a new observational window into
+
-the early Universe approximately one billion years after the Big
+
-Bang. During this era, the radiation from the first stars and galaxies
+
-pushes the spin temperature out of equilibrium before heating and
+// The hyperfine transition of neutral hydrogen generates photons at
-eventually ionising the neutral hydrogen of the intergalactic medium
+// the wavelength of 21 cm, opening a new observational window into
-(IGM). Next to the source properties, the 21-cm signal depends on
+// the early Universe approximately one billion years after the Big
-the clustering and temperature distribution of the neutral gas, the
+// Bang. During this era, the radiation from the first stars and galaxies
-primordial background radio emission, and the detailed interaction
+// pushes the spin temperature out of equilibrium before heating and
-processes between radiation and matter. It is therefore not surprising
+// eventually ionising the neutral hydrogen of the intergalactic medium
-that the 21-cm radiation from the cosmic dawn contains a wealth of
+// (IGM). Next to the source properties, the 21-cm signal depends on
-information about the properties of the first stars (Fialkov & Barkana
+// the clustering and temperature distribution of the neutral gas, the
-2014; Mirocha et al. 2018; Ventura et al. 2023; Sartorio et al. 2023),
+// primordial background radio emission, and the detailed interaction
-galaxies (Park et al. 2019; Reis et al. 2020; Hutter et al. 2021), and
+// processes between radiation and matter. It is therefore not surprising
-black holes (Pritchard & Furlanetto 2007; Ross et al. 2019). It can
+// that the 21-cm radiation from the cosmic dawn contains a wealth of
-furthermore be used to constrain the cosmological model (Liu &
+// information about the properties of the first stars (Fialkov & Barkana
-Parsons 2016; Schneider et al. 2023; Shmueli et al. 2023) and, in
+// 2014; Mirocha et al. 2018; Ventura et al. 2023; Sartorio et al. 2023),
-particular, the dark sector, such as the nature of dark matter (Sitwell
+// galaxies (Park et al. 2019; Reis et al. 2020; Hutter et al. 2021), and
-et al. 2014; Chatterjee et al. 2019; Nebrin et al. 2019; Muñoz et al.
+// black holes (Pritchard & Furlanetto 2007; Ross et al. 2019). It can
-2020; Jones et al. 2021; Giri & Schneider 2022; Hotinli et al. 2022;
+// furthermore be used to constrain the cosmological model (Liu &
-Flitter & Kovetz 2022; Hibbard et al. 2022), interactions between
+// Parsons 2016; Schneider et al. 2023; Shmueli et al. 2023) and, in
-the dark and visible sector (Barkana et al. 2018; Fialkov et al. 2018;
+// particular, the dark sector, such as the nature of dark matter (Sitwell
-Kovetz et al. 2018; Lopez-Honorez et al. 2019; Mosbech et al. 2023),
+// et al. 2014; Chatterjee et al. 2019; Nebrin et al. 2019; Muñoz et al.
-or potential exotic decay and annihilation processes (D’Amico et al.
+// 2020; Jones et al. 2021; Giri & Schneider 2022; Hotinli et al. 2022;
-2018; Liu & Slatyer 2018; Mitridate & Podo 2018).
+// Flitter & Kovetz 2022; Hibbard et al. 2022), interactions between
-Reliable detection of the 21-cm signal at these redshifts has yet to
+// the dark and visible sector (Barkana et al. 2018; Fialkov et al. 2018;
-be achieved, but ongoing experiments, such as the Giant Metrewave
+// Kovetz et al. 2018; Lopez-Honorez et al. 2019; Mosbech et al. 2023),
-Radio Telescope (GMRT, Paciga et al. 2013), the Precision Array for
+// or potential exotic decay and annihilation processes (D’Amico et al.
-Probing the Epoch of Reionization (PAPER, Kolopanis et al. 2019),
+// 2018; Liu & Slatyer 2018; Mitridate & Podo 2018).
-the Murchison Widefield Array (MWA, Trott et al. 2020), the Low-
+// Reliable detection of the 21-cm signal at these redshifts has yet to
-Frequency ARray (LOFAR, Mertens et al. 2020), and the Hydrogen
+// be achieved, but ongoing experiments, such as the Giant Metrewave
-Epoch of Reionization Array (HERA, The HERA Collaboration et al.
+// Radio Telescope (GMRT, Paciga et al. 2013), the Precision Array for
-2023) have provided upper limits on the 21-cm power spectrum for
+// Probing the Epoch of Reionization (PAPER, Kolopanis et al. 2019),
-a broad range of redshifts. These bounds have been used to exclude
+// the Murchison Widefield Array (MWA, Trott et al. 2020), the Low-
-regions of the parameter space describing extreme properties of the
+// Frequency ARray (LOFAR, Mertens et al. 2020), and the Hydrogen
-IGM during the epoch of reionisation (Ghara et al. 2020, 2021; Greig
+// Epoch of Reionization Array (HERA, The HERA Collaboration et al.
-et al. 2021a,b; The HERA Collaboration et al. 2022a).
+// 2023) have provided upper limits on the 21-cm power spectrum for
-The Square Kilometre Array (SKA), a next-generation radio in-
+// a broad range of redshifts. These bounds have been used to exclude
-terferometer, is currently under construction in South Africa and
+// regions of the parameter space describing extreme properties of the
-Western Australia. Its low-frequency component, SKA-low, has the
+// IGM during the epoch of reionisation (Ghara et al. 2020, 2021; Greig
-capability to not only measure the 21-cm power spectrum with high
+// et al. 2021a,b; The HERA Collaboration et al. 2022a).
-signal-to-noise ratio but also provide sky images at redshifts around2
+// The Square Kilometre Array (SKA), a next-generation radio in-
-T. Schaeffer et al.
+// terferometer, is currently under construction in South Africa and
-𝑧 ≈ 5 − 25 (e.g. Mellema et al. 2015; Wyithe et al. 2015; Ghara
+// Western Australia. Its low-frequency component, SKA-low, has the
-et al. 2017; Giri et al. 2018a; Bianco et al. 2021b). The potential
+// capability to not only measure the 21-cm power spectrum with high
-of SKA-low for studying the cosmic dawn and reionization era has
+// signal-to-noise ratio but also provide sky images at redshifts around2
-been extensively investigated in various studies, exploring properties
+// T. Schaeffer et al.
-of the ionizing sources and the ionization structure of the universe
+// 𝑧 ≈ 5 − 25 (e.g. Mellema et al. 2015; Wyithe et al. 2015; Ghara
-(e.g. Giri et al. 2018b; Zackrisson et al. 2020; Giri & Mellema 2021;
+// et al. 2017; Giri et al. 2018a; Bianco et al. 2021b). The potential
-Gazagnes et al. 2021; Bianco et al. 2023). These studies highlight
+// of SKA-low for studying the cosmic dawn and reionization era has
-the significant role that SKA-low will play in advancing our under-
+// been extensively investigated in various studies, exploring properties
-standing of these critical cosmic epochs.
+// of the ionizing sources and the ionization structure of the universe
-Next to the tremendous experimental effort, accurate and reliable
+// (e.g. Giri et al. 2018b; Zackrisson et al. 2020; Giri & Mellema 2021;
-theoretical methods to model the 21-cm signal at the required accu-
+// Gazagnes et al. 2021; Bianco et al. 2023). These studies highlight
-racy level are currently being developed. Modelling the 21-cm signal
+// the significant role that SKA-low will play in advancing our under-
-is challenging as it involves a broad dynamical range from minihaloes
+// standing of these critical cosmic epochs.
-to cosmological scales. It depends on the details of hydrodynamical
+// Next to the tremendous experimental effort, accurate and reliable
-feedback processes for galaxies, the propagation of radiation through
+// theoretical methods to model the 21-cm signal at the required accu-
-large cosmological scales, and the detailed interaction processes of
+// racy level are currently being developed. Modelling the 21-cm signal
-photons with gas particles of the IGM (e.g., Iliev et al. 2006; Mellema
+// is challenging as it involves a broad dynamical range from minihaloes
-et al. 2006b; Trac & Cen 2007).
+// to cosmological scales. It depends on the details of hydrodynamical
-One option is to predict the 21-cm signal with the help of coupled
+// feedback processes for galaxies, the propagation of radiation through
-radiative-transfer hydrodynamic simulations, some well-known ex-
+// large cosmological scales, and the detailed interaction processes of
-amples being the Cosmic Dawn (CoDA) (Ocvirk et al. 2016; Ocvirk
+// photons with gas particles of the IGM (e.g., Iliev et al. 2006; Mellema
-et al. 2020; Lewis et al. 2022), the 21SSD (Semelin et al. 2017),
+// et al. 2006b; Trac & Cen 2007).
-and the THESAN simulations (Kannan et al. 2022; Garaldi et al.
+// One option is to predict the 21-cm signal with the help of coupled
-2022). Another option is to post-process N-body simulations with
+// radiative-transfer hydrodynamic simulations, some well-known ex-
-ray-tracing algorithms, such as the Conservative, Causal Ray-tracing
+// amples being the Cosmic Dawn (CoDA) (Ocvirk et al. 2016; Ocvirk
-code (C2 RAY; Mellema et al. 2006a) or the Cosmological Radiative
+// et al. 2020; Lewis et al. 2022), the 21SSD (Semelin et al. 2017),
-transfer Scheme for Hydrodynamics (CRASH; Maselli et al. 2003).
+// and the THESAN simulations (Kannan et al. 2022; Garaldi et al.
-Full radiative-transfer numerical methods are fundamental to un-
+// 2022). Another option is to post-process N-body simulations with
-derstanding the 21-cm signal and estimating the accuracy of more
+// ray-tracing algorithms, such as the Conservative, Causal Ray-tracing
-approximate methods. However, they are very computationally ex-
+// code (C2 RAY; Mellema et al. 2006a) or the Cosmological Radiative
-pensive and can hardly be used to scan the vast cosmological and
+// transfer Scheme for Hydrodynamics (CRASH; Maselli et al. 2003).
-astrophysical parameter space. To perform Bayesian inference anal-
+// Full radiative-transfer numerical methods are fundamental to un-
-ysis on a mock 21-cm data set, semi-numerical algorithms are often
+// derstanding the 21-cm signal and estimating the accuracy of more
-used, better suited to generate thousands of realizations of the sig-
+// approximate methods. However, they are very computationally ex-
-nal itself. They rely on the excursion set formalism (Furlanetto et al.
+// pensive and can hardly be used to scan the vast cosmological and
-2004), such as 21cmFAST (Mesinger et al. 2011) or SIMFAST21 (San-
+// astrophysical parameter space. To perform Bayesian inference anal-
-tos et al. 2010).
+// ysis on a mock 21-cm data set, semi-numerical algorithms are often
-In this paper, we present the new framework BEoRN which stands
+// used, better suited to generate thousands of realizations of the sig-
-for Bubbles during the Epoch of Reionisation Numerical simulator.
+// nal itself. They rely on the excursion set formalism (Furlanetto et al.
-The code is based on a one-dimensional radiative transfer method
+// 2004), such as 21cmFAST (Mesinger et al. 2011) or SIMFAST21 (San-
-in which interactions between matter and radiation are treated in a
+// tos et al. 2010).
-spherically symmetric way around sources. This approach is signifi-
+// In this paper, we present the new framework BEoRN which stands
-cantly faster than full 3-d radiative transfer codes and arguably more
+// for Bubbles during the Epoch of Reionisation Numerical simulator.
-precise than semi-numerical algorithms which are not based on indi-
+// The code is based on a one-dimensional radiative transfer method
-vidual sources. In this aspect, BEoRN is similar to other existing codes
+// in which interactions between matter and radiation are treated in a
-such as BEARS (Thomas et al. 2009) or GRIZZLY (Ghara et al. 2018).
+// spherically symmetric way around sources. This approach is signifi-
-However, in contrast to other 1d radiative transfer codes, BEoRN self-
+// cantly faster than full 3-d radiative transfer codes and arguably more
-consistently accounts for the evolution of individual sources during
+// precise than semi-numerical algorithms which are not based on indi-
-the emission of photons. This includes both the redshifting of pho-
+// vidual sources. In this aspect, BEoRN is similar to other existing codes
-tons due to the expansion of space and the increase of luminosity
+// such as BEARS (Thomas et al. 2009) or GRIZZLY (Ghara et al. 2018).
-caused by the growth of individual sources over time. Both effects
+// However, in contrast to other 1d radiative transfer codes, BEoRN self-
-have a non-negligible influence on the radiation profile surrounding
+// consistently accounts for the evolution of individual sources during
-sources.
+// the emission of photons. This includes both the redshifting of pho-
-The BEoRN framework allows for a flexible parametrisation to
+// tons due to the expansion of space and the increase of luminosity
-model any source of radiation, such as e.g. Pop-III stars, galaxies,
+// caused by the growth of individual sources over time. Both effects
-or quasars. It produces a 3-dimensional (3D) light-cone realisation
+// have a non-negligible influence on the radiation profile surrounding
-of the 21-cm signal from the cosmic dawn to the end of reionisation
+// sources.
-including redshift space distortion effects. The underlying gas density
+// The BEoRN framework allows for a flexible parametrisation to
-field as well as the position of sources is directly obtained from
+// model any source of radiation, such as e.g. Pop-III stars, galaxies,
-outputs of an 𝑁-body simulation. We have designed BEoRN to be
+// or quasars. It produces a 3-dimensional (3D) light-cone realisation
-user-friendly and modular so that it can be applied in combination
+// of the 21-cm signal from the cosmic dawn to the end of reionisation
-with different gravity solvers or source models, for example.
+// including redshift space distortion effects. The underlying gas density
-MNRAS 000, 1–18 (2023)
+// field as well as the position of sources is directly obtained from
-The paper is structured as follows: Section 2 describes the BEoRN
+// outputs of an 𝑁-body simulation. We have designed BEoRN to be
-code, while section 3 validates it by comparing its predictions with
+// user-friendly and modular so that it can be applied in combination
-the publicly available 21cmFAST code. In section 4, three benchmark
+// with different gravity solvers or source models, for example.
-models are presented, calibrated to the latest observations, and the
+// MNRAS 000, 1–18 (2023)
-evolution of the 21-cm signal during the cosmic dawn and epoch
+// The paper is structured as follows: Section 2 describes the BEoRN
-of reionization is studied. The work concludes with a summary and
+// code, while section 3 validates it by comparing its predictions with
-conclusion in section 5.
+// the publicly available 21cmFAST code. In section 4, three benchmark
-Note that throughout the paper, physical distance units are specified
+// models are presented, calibrated to the latest observations, and the
-with the prefix "𝑝", while co-moving distance units are specified
+// evolution of the 21-cm signal during the cosmic dawn and epoch
-with the prefix "𝑐". The cosmological parameters used in this work
+// of reionization is studied. The work concludes with a summary and
-are consistent with Planck 2018 results (Planck Collaboration et al.
+// conclusion in section 5.
-2020), namely matter abundance Ωm = 0.31, baryon abundance
+// Note that throughout the paper, physical distance units are specified
-Ωb = 0.045, and dimensionless Hubble constant ℎ = 0.68. The
+// with the prefix "𝑝", while co-moving distance units are specified
-standard deviation of matter perturbations at 8ℎ −1 cMpc scale is
+// with the prefix "𝑐". The cosmological parameters used in this work
-𝜎8 = 0.81.
+// are consistent with Planck 2018 results (Planck Collaboration et al.
+// 2020), namely matter abundance Ωm = 0.31, baryon abundance
+// Ωb = 0.045, and dimensionless Hubble constant ℎ = 0.68. The
+// standard deviation of matter perturbations at 8ℎ −1 cMpc scale is
+// 𝜎8 = 0.81.

main.typ

@@ -1,7 +1,6 @@
 #import "template/template.typ": *
 #import "@preview/muchpdf:0.1.1": muchpdf
 
-
 // Patch the ETH logo to actually be white:
 #let logo = "assets/eth-logo.svg"
 #let original = read(logo)
@@ -14,42 +13,50 @@
   image(bytes(changed)),
   image("assets/uzh-logo.svg")
 )
-
+#set math.equation(numbering: "(1)", supplement: [Eq.])
 #show: tasteful-thesis.with(
-  title: "Refinements of BEoRN",
+  // title: "BEoRN version 2",
-  subtitle: "Self-consistent semi-numerical simulation of the epoch of reionization",
+  title: "Simulating the EOR with self-consistent growth of galaxies",
   authors: ("Rémy Moll",),
+  supervisors: ("Prof. Aurel Schneider",),
   affiliation: "ETH Zürich, Universität Zürich",
   abstract: include("abstract.typ"),
   background-color: color.rgb(32, 64, 123),
   logos: logos,
-  background-image: image("assets/background.png"),
+  // background-image: image("assets/background.png"),
+  background-image: image("assets/bg-desat.jpg"),
   date: datetime.today().display("[day]. [month repr:long] [year]"),
   font: "FreeSans",
   pre_content: muchpdf(read("assets/declaration-originality.pdf", encoding: none)),
-
 )
 
 
+
 //
 // Content
 //
 
-Stars form early #cite(<10.1093>, form: "normal") but  @10.1093 state that they are bright.
+// Stars form early #cite(<10.1093>, form: "normal") but  @10.1093 state that they are bright.
 
 
+// #import "importer/main.typ": *
+// #let notebook = json("../workdir/00_baseline/reference_painting.ipynb")
+
+// #code_cell(notebook, cell_id: "handler")
+// #image_cell(notebook, cell_id: "profile_plot")
+// #image_cell(notebook, cell_id: "profile_plot_2")
+
 
 #include "introduction.typ"
 #include "procedure.typ"
 #include "halo_mass_history.typ"
 #include "implementation.typ"
 #include "validation.typ"
-// Maybe no validation?
 #include "results.typ"
-#include "outlook.typ"
+// #include "outlook.typ"
 #include "conclusion.typ"
-#include "acknowledgements.typ"
 
+#include "acknowledgements.typ"
 
 #bibliography("references.bib", style: "assets/the-astrophysical-journal.csl")
 

outlook.typ

@@ -1 +1,12 @@
+#import "importer/main.typ": *
+#import "helpers.typ": *
+
 = Outlook
+
+
+- implement merger tree growth fitting based on a more sophisiticated growth model (e.g. based on the PS formalism)
+-
+
+- The sensitivity of the results to the growth rate suggest that more refined halo finding and growth tracking algorithms should be investigated
+Where is rockstar?
+

procedure.typ

@@ -1,6 +1,73 @@
-= Overview of the BEoRN simulation procedure
+#import "importer/main.typ": *
-This section describes the full procedure for a single simulation run of the BEoRN simulation suite, as well as the necessary adaptations to reflect the refined underlying model.
+#import "helpers.typ": *
+#import "@preview/physica:0.9.5": *
+
+= Overview of the #beorn framework <procedure>
+
+This section describes the procedure for a full simulation run of the #beorn simulation suite, including the underlying modelling of the radiation sources. The code of #beorn as well as usage instructions are publicly available under #link("https://github.com/cosmic-reionization/BEoRN", "https://github.com/cosmic-reionization/BEoRN")#footnote[
+  For an explicit overview of the changes referenced here, please refer to #link("https://github.com/moll-re/BEoRN")
+].
+
+
+
+== The halo mass model of reionization <hmreio>
+
+The central action
+// don't like that word
+performed by #beorn is the parametrization of sources of ionizing radiation through the properties of their host dark matter halos. This approach is based on the model presented by @schneider2023cosmologicalforecast21cmpower and gives a description
+// bad word
+of the $21 "cm"$ signal through the treatment of flux profiles around sources. Using these overlying profiles allows to efficiently compute the ionization state of the intergalactic medium (IGM) without the need for computationally expensive radiative transfer simulations.
+
+The model assumes that the radiation sources are hosted by dark matter halos and expresses the star formation and radiation properties as a function of the halo mass $M_"h"$ and mass accretion rate $dot(M_"h")$. The modelling of the halo mass evolution is subject to a detailed discussion in section @halo_mass_history, for the purpose of the model an arbitrary halo mass accretion history $M_"h" (z)$ is assumed to be known.
+
+star formation rate
+$
+  dot(M)_star = f_star (M_"h") dot dot(M_"h")
+$ <eq:star_formation_rate>
+The star formation efficiency $f_star$ is explained by @Schaeffer_2023
+
+
+=== Expression of the profiles
+$
+  derivative(V, t) = dot(N)_"ion"(t) / overline(n)_H^0 - alpha_B dot C / a^3 dot overline(n)_H^0 dot V
+$
+
+Lyman-alpha photons induce a coupling between the spin temperature and the kinetic temperature of the gas. This effect, known as the Wouthuysen-Field effect
+#cite(<Wouthuysen>, form: "normal")
+#cite(<Field>, form: "normal")
+causes absorption of $21 "cm"$ photons before reionization. This is reflected in the absorption expected in the global signal before reionization.
+$
+  rho_alpha (r bar M, z) = (1 + z)^2 / (4 pi r^2) dot sum_(n=2)^(n_m)f_n dot epsilon_alpha (nu prime) dot f_star dot dot(M)(z prime bar M, z)
+$
+
+
+
+The temperature around the sources is described
+// bad word
+by the cooling temperature of the adiabatically expanding universe and the heating due to X-ray photons emitted by the newly formed stars. The temperature profile follows
+
+$
+  3/2 dot derivative(rho_h (r bar M, z), z) = (3 rho_h (r bar M, z)) / (1 + z) - (rho_"xray" (r bar M, z)) /(k_B (1 + z) H(z))
+$
+which is based on ????
+
+
+
+Ionizing photons, i.e. photons with energies above $13.6 "eV"$ experience a large optical depth which justifies the expression
+$
+x_("HII")(r bar M, z) = theta_"H" (R_b (M, z) - r) = theta_"H" (root(3, 3/ (4pi) V(M,z))
+ -r )
+$
+
+// introduced inaccuracies
+// e.g. papers like "2309...." suggest a revised halo mass growth.
+// e.g. bursty star formation as presented by Romain Teyssier
 
 == Simulation steps
 
-The code of BEoRN as well as a comprehensive documentation are publicly available under #link("https://github.com/cosmic-reionization/BEoRN", "https://github.com/cosmic-reionization/BEoRN").
+=== Halo catalog - n body simulations
+
+=== Computation of radiation profiles
+
+=== Optimized painting with the parallel+binned approach
+

references.bib

@@ -16,7 +16,7 @@
 
 
 
-
+### The three main THESAN papers
 
 @article{Kannan_2021,
    title={Introducing the <scp>thesan</scp> project: radiation-magnetohydrodynamic simulations of the epoch of reionization},
@@ -29,10 +29,8 @@
    publisher={Oxford University Press (OUP)},
    author={Kannan, R and Garaldi, E and Smith, A and Pakmor, R and Springel, V and Vogelsberger, M and Hernquist, L},
    year={2021},
-   month=dec, pages={4005–4030} }
+   month=dec, pages={4005–4030}
-
+}
-
-
 @article{Garaldi_2022,
    title={The<scp>thesan</scp>project: properties of the intergalactic medium and its connection to reionization-era galaxies},
    volume={512},
@@ -44,9 +42,8 @@
    publisher={Oxford University Press (OUP)},
    author={Garaldi, E and Kannan, R and Smith, A and Springel, V and Pakmor, R and Vogelsberger, M and Hernquist, L},
    year={2022},
-   month=feb, pages={4909–4933} }
+   month=feb, pages={4909–4933}
-
+}
-
 @article{Smith_2022,
    title={The<scp>thesan</scp>project: Lyman-α emission and transmission during the Epoch of Reionization},
    volume={512},
@@ -58,4 +55,65 @@
    publisher={Oxford University Press (OUP)},
    author={Smith, A and Kannan, R and Garaldi, E and Vogelsberger, M and Pakmor, R and Springel, V and Hernquist, L},
    year={2022},
-   month=mar, pages={3243–3265} }
+   month=mar, pages={3243–3265}
+}
+
+
+
+
+### Beorn specific
+# original beorn paper
+@article{Schaeffer_2023,
+   title={<scp>beorn</scp>: a fast and flexible framework to simulate the epoch of reionization and cosmic dawn},
+   volume={526},
+   ISSN={1365-2966},
+   url={http://dx.doi.org/10.1093/mnras/stad2937},
+   DOI={10.1093/mnras/stad2937},
+   number={2},
+   journal={Monthly Notices of the Royal Astronomical Society},
+   publisher={Oxford University Press (OUP)},
+   author={Schaeffer, Timothée and Giri, Sambit K and Schneider, Aurel},
+   year={2023},
+   month=sep, pages={2942–2959} }
+
+
+# theoretical foundation - halo model of reionization
+@misc{schneider2023cosmologicalforecast21cmpower,
+      title={Cosmological forecast of the 21-cm power spectrum using the halo model of reionization},
+      author={Aurel Schneider and Timothée Schaeffer and Sambit K. Giri},
+      year={2023},
+      eprint={2302.06626},
+      archivePrefix={arXiv},
+      primaryClass={astro-ph.CO},
+      url={https://arxiv.org/abs/2302.06626},
+}
+
+
+
+
+
+
+# Wouthuysen-Field effect
+@ARTICLE{Wouthuysen,
+       author = {{Wouthuysen}, S.~A.},
+        title = "{On the excitation mechanism of the 21-cm (radio-frequency) interstellar hydrogen emission line.}",
+      journal = {\aj},
+         year = 1952,
+        month = jan,
+       volume = {57},
+        pages = {31-32},
+          doi = {10.1086/106661},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1952AJ.....57R..31W},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{Field,
+  author={Field, George B.},
+  journal={Proceedings of the IRE},
+  title={Excitation of the Hydrogen 21-CM Line},
+  year={1958},
+  volume={46},
+  number={1},
+  pages={240-250},
+  keywords={Hydrogen;Clouds;Electromagnetic wave absorption;Kinetic theory;Equations;Deuterium;Temperature distribution;Observatories;Electrons;Atomic measurements},
+  doi={10.1109/JRPROC.1958.286741}}

results.typ

@@ -0,0 +1,31 @@
+#import "importer/main.typ": *
+#let notebook = json("../workdir/11_visualization/simulation_outputs.ipynb")
+
+= Results <results>
+
+
+Comparison of different runs and their effect, esp. on the power spectrum.
+Importance of RSD for the 21 cm signal
+https://arxiv.org/abs/2011.03558
+
+
+== Effect on the global signal
+#figure(
+  image_cell(notebook, cell_id: "global_signal_combined"),
+  caption: "???",
+
+) <fig:global_signal_combined>
+
+Try to isolate global effects and line out the map-level differences.
+
+== Map-level investigation
+
+#figure(
+  image_cell(notebook, cell_id: "grids_and_diffs"),
+  caption: "???",
+
+) <fig:grids_and_diffs>
+
+
+== Statistics
+Also compare summary statistics like the power spectrum.

template/template.typ

@@ -29,10 +29,13 @@
   //
   set document(author: authors, title: title, description: subtitle)
 
+  // Set body font family.
+  set text(font: font, 11pt)
+  show heading: set text(font: font, fill: background-color)
+
   let font-color = color;
   // Check if the background color is closer to black or white
   let components = background-color.components()
-  // show the components for debugging
   let luminance = float(0.299 * components.at(0) + 0.587 * components.at(1) + 0.114 * components.at(2))
   if luminance > 0.5 {
     font-color = color.black
@@ -41,41 +44,54 @@
   }
 
 
-  //customize look of figure
+  // color links
-  // set figure.caption(separator: [ --- ], position: top)
-
-  //customize inline raw code
-  show raw.where(block: false) : it => h(0.5em) + box(fill: color.lighten(90%), outset: 0.2em, it) + h(0.5em)
-
-  // Set body font family.
-  set text(font: font, 12pt)
-  show heading: set text(font: font, fill: background-color)
-
-  // add space for heading
-  show heading.where(level:1): it => it + v(0.5em)
-
-  // Set link style
   show link: it => underline(text(fill: background-color, it))
-
   show ref: it => text(fill: background-color, it)
-
   show ref.where(): it => text(fill: background-color, it)
 
-  //numbered list colored
+  // colors lists
   set enum(indent: 1em, numbering: n => [#text(fill: background-color, numbering("1.", n))])
-
-  //unordered list colored
   set list(indent: 1em, marker: n => [#text(fill: background-color, "•")])
 
 
-
+  // citation style
   set cite(
     form: "prose"
   )
+  // add space for heading
+  show heading.where(level:1): it => it + v(0.5em)
+
+  //
+  // Included content
+  //
+
+  // figures
+  // set figure.caption(separator: [ --- ], position: top)
+
+  // code blocks
+  show raw.where(block: true) : it => h(0.5em) + box(fill: background-color.lighten(80%), outset: 0.5em, width: 100%, it) + h(0.5em)
 
 
-  // display of outline entries
+
-  show outline.entry: it => text(size: 12pt, weight: "regular",it)
+  let authors_block(authors, denomination: "Author") = {
+    if authors.len() == 0 {
+      return
+    }
+    let prefix = denomination
+    if authors.len() > 2 {
+      prefix += "s"
+    }
+
+    stack(
+      dir: ltr,
+      text(prefix + ": ", weight: 600),
+      stack(
+        dir: ttb,
+        spacing: 0.5em,
+        ..authors
+      )
+    )
+  }
 
   //
   // Title page
@@ -93,16 +109,19 @@
     background-image
   )
 
+  //  define the base widht of a tile, as a tenth of the page width
+  let tile_width = 1.51cm
+
   // Add a tiling of white squares over the background to simulate a grid
   for i in range(0, 14) {
     for j in range(0, 14) {
       place(
         bottom + right,
-        dx: -i * 3.55em + 0.1em,
+        dx: -i * tile_width + 0.1em,
-        dy: -j * 3.55em,
+        dy: -j * tile_width,
       )[
         #square(
-          size: 3.55em,
+          size: tile_width,
           // fill: gradient.linear(
           //   color.white,
           //   color.black.transparentize(0%),
@@ -177,7 +196,6 @@
     ),
   )
 
-
   // add a few more tiles *above* the background image to simulate a grid structure
   let draw_pairs = (
     (0, 10),
@@ -261,19 +279,11 @@
   for (i, j) in draw_pairs {
     place(
       bottom + right,
-      dx: -i * 3.55em + 0.1em,
+      dx: -i * tile_width + 0.1em,
-      dy: -j * 3.55em,
+      dy: -j * tile_width,
     )[
       #square(
-        size: 3.55em,
+        size: tile_width,
-        // fill: gradient.linear(
-        //   color.white,
-        //   color.black.transparentize(0%),
-        //   color.black.transparentize(0%),
-        //   color.black.transparentize(0%),
-        //   color.black.transparentize(0%),
-        //   angle: 45deg,
-        // ),
         fill: none,
         stroke: (
           paint: color.white,
@@ -281,7 +291,6 @@
         )
       )
     ]
-
   }
 
 
@@ -290,17 +299,24 @@
     x: 4em,
     y: 4em,
   )[
-    #align(center, text(font: font, 3em, weight: 700, title, fill: font-color))
+    #set text(font: font, fill: font-color)
-    #v(2em, weak: true)
+    #align(center, text(title, size: 2.5em, weight: 600))
     #if subtitle != none {
-      align(center, text(font: font, 2em, weight: 600, subtitle, fill: font-color))
+      v(1.5em, weak: true)
+      align(center, text(subtitle, size: 2em, weight: 500))
     }
-    #v(2em, weak: true)
+    #pad(
-    #align(
+      x: 6em,
-      center,
+      y: 0em,
-      text(font: font, 1em, authors.join(", "), fill: font-color)
+    )[
+      #stack(
+        dir: ltr,
+        authors_block(authors),
+        h(1fr),
+        authors_block(supervisors, denomination: "Supervisor")
       )
     ]
+  ]
 
 
   let padded_logos = logos.map(logo => pad(x: 0.2cm, logo))
@@ -355,14 +371,12 @@
     footer: footer,
     margin: 4em,
   )
+  counter(page).update(1)
 
   //
-  // Table of contents.
+  // "First" page - abstract and TOC
   //
 
-
-
-
   abstract
   v(2em)
   outline()
@@ -374,36 +388,8 @@
   // Main body.
   //
   set heading(numbering: "1.")
-
   set par(justify: true)
 
   body
 }
 
-
-  // let footer = grid(
-  //   rows: auto,
-  //   v(0mm),
-  //   line(length: 100%, stroke: 0.6pt), // should be 1.6pt according to guidelines
-  //   v(2.5mm),
-  //   text(
-  //       font: "Roboto",
-  //       stretch: 100%,
-  //       fallback: false,
-  //       weight: "regular",
-  //       size: 10pt
-  //   )[
-  //     #set align(right)
-  //     // context needed for page counter for typst >= 0.11.0
-  //     #context [
-  //       #let counter_disp = counter(page).display()
-  //       //#hide(counter_disp)
-  //       //#counter_disp
-  //       #context {
-  //         let after_table_of_contents = query(selector(<__after_table_of_contents>).before(here())).len() >= 1
-  //         if after_table_of_contents {counter_disp}
-  //         else {hide(counter_disp)}
-  //       }
-  //     ]
-  //   ]
-  // )

validation.typ

@@ -1 +1,19 @@
-= Validation
+= Validation <validation>
+We perform several validation tests to ensure the accuracy and reliability of our simulation results. This section details both code-level tests and scientific validations against established results.
+
+- Comparison to old (simplified) run!
+- Comparison to THESAN
+
+== Code validation
+We ensure consistency of the updated BEoRN code with previous versions by running a series of simulations under identical conditions. We compare key outputs starting from the profiles of individuall sources, to the ionization maps, and finally to the global reionization signals. This step-by-step comparison allows us to identify any discrepancy that may arise from the code changes.
+
+Similarly we maintain backward compatibility with the input format used in previous BEORN runs (i.e. snapshots generated by pkdgrav or 21cmfast). This allows us to reproduce the earlier runs and match the results as described by @Schaeffer_2023.
+
+== Convergence tests
+To ensure that our results are not sensitive to the numerical resolution of the simulation, we perform convergence tests. We compare the following variations of resolution: Firstly we compare effects of the grid resolution by running simulations with $128^3$, $256^3$, and $512^3$ cells. Secondly we investigate the impact of the mass resolution by comparing the results obtained from the #smallcaps[Thesan-Dark] 1 and 2 simulations, which have different particle masses, as mentioned in @procedure.
+
+
+
+== Scientific validation?
+Against THESAN runs
+// Probably not happening!