nearly fully fleshed out now

backup.typ

@@ -1,9 +1,50 @@
 #import "globals.typ": *
 
 
+== Full profiles <backup_full_profiles>
+$
+  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)
+$
+with the lookback redshift $z prime$ so $nu prime = nu dot (1+z prime) slash (1+z)$
+
+$=>$ coupling coefficient
+$
+  x_alpha (r bar M, z) = (1.81 dot 10^11) / (1 + z) dot S_alpha (z) dot rho_alpha (r bar M, z)
+$
+with a suppression factor $S_alpha (z)$
+
+
+#pagebreak()
+$
+  rho_"xray" (r bar M, z) = 1 / r^2 sum_i f_i f_(X,h) dot integral_(nu^i_"th")^oo d nu (nu - nu^i_"th") h_P sigma_i (nu) e^(-tau_nu) f_star dot(M) (z prime bar M, z)
+$
+$
+  ==> 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))
+$
+with the Boltzmann constant $k_B$ and $H(z)$ is the Hubble parameter
+// where i={H, He} and νi thhP ={13.6, 26.5} eV.
+// Contribution from both He and H since
+// No defined sum but integral due to all radiations being xray
+
+// Lookback comes from the definition of comoving r:
+// $r = integral_(z)^(z prime) c dz dot (1+z) / H(z)$
+
+#pagebreak()
+
+The comoving ionized volume around a source of ionizing photons satisfies the differential equation
+$
+  derivative(V, t) = dot(N)_"ion"(t) / overline(n)_H^0 - alpha_B dot C / a^3 dot overline(n)_H^0 dot V
+$
+bubble radius $R_b = root(3, 3/ (4pi) V(M,z))$ and using the Heaviside step function $theta_H$:
+$
+  x_("HII")(r bar M, z) = theta_"H" lr([R_b (M, z) - r], size: #150%)
+$
+
+
 == Validation <backup_validation>
-#[
+#line(length: 100%, stroke: 0pt)
-  #set image(height: 45%, fit: "contain")
+#align(center)[
+  #set image(height: 43%, fit: "contain")
   #let notebook = json("../workdir/11_visualization/validation_simple_run.ipynb")
   #image_cell(notebook, cell_id: "validation_signal_comparison_old_v_new")
 
@@ -13,11 +54,11 @@
 
 
 
-== Backup slides
+== Thesan resolution issues
-This is a backup slide
+#let notebook = json("../workdir/11_visualization/halo_mass_function_thesan_1_2.ipynb")
-#lorem(50)
-
-== Another backup slide
-#lorem(50)
 
+#line(length: 100%, stroke: 0pt)
+#align(center)[
+  #image_cell(notebook, cell_id: "halo_mass_functions")
+]
 

beorn.typ

@@ -38,9 +38,9 @@
 #pinit-point-to(
   (1, 2),
   pin-dx: 20pt,
-  pin-dy: -20pt,
+  pin-dy: -30pt,
   body-dx: -70pt,
-  body-dy: -80pt,
+  body-dy: -95pt,
   offset-dx: 20pt,
   offset-dy: 30pt,
 )[spherical symmetry]
@@ -50,12 +50,12 @@
 #pinit-point-to(
   (3, 4),
   pin-dx: 20pt,
-  pin-dy: -20pt,
+  pin-dy: -30pt,
-  body-dx: -90pt,
+  body-dx: -70pt,
-  body-dy: -80pt,
+  body-dy: -95pt,
   offset-dx: 20pt,
   offset-dy: 30pt,
-)[convolution (fft)]
+)[convolution (`FFT`)]
 
 
 #pagebreak()

conclusion.typ

@@ -2,14 +2,37 @@
 
 = Conclusion
 == Summary
-- We presented Beorn, a new code to simulate the 21cm signal from the EoR and Cosmic Dawn.
+- #beorn a semi-numerical tool to simulate the 21-cm signal
-- Beorn is based on the halo model and uses a novel approach to compute the 21cm signal from 1D profiles around individual sources.
+
-- Beorn is fast, flexible, and easy to use.
+  - uses the _halo model of reionization_
-- We validated Beorn against numerical simulations and showed that it can reproduce their results with good accuracy.
+  - describes sources in terms of their host DM halo
-- Beorn is publicly available and can be used for a variety of applications, including forecasting, parameter estimation, and data analysis.
+  - $=>$ central dependence on halo growth
+  // since it affects the SFR and thus the emissivity
+
+- more accurate treatment of *individual* mass accretion
+  // change in profiles trivially
+  - leads to significant changes to reionization history
+  // which could in theory be absorbed by shifting other paremeters
+  - map-level fluctuations
+  // which we can hope to observe (although many are subtle)
+
+// unique position of 21-cm cosmology -> cannot discuss observational constraints
+
+- #beorn python package: #link("https://github.com/cosmic-reionization/beorn")
+  // invite you to check out
+  - simulation-agnostic
+  - easier to use
+  - fully parallelized
+
+
+== Outlook
+- further validation
+// finally ready for direct comparison with c2ray? now that parameters and loading have been properly implemented
 
-== Upcoming improvements
 - investigation + parameterization of stochasticity
-- application to larger volumes
+// Assuming other relations related to production of photons is (hopefully by now well motivated) complex
-- fully parallel runs
+// these cannot directly be inferred => expressed as a distribution as a function of another halo property
 
+- application to larger volumes
+// the scale-up -> large volumes with usable merger trees
+// comitting to reserving some 100s of node hours (which I would still quantify as fast)

halo_model.typ

@@ -3,7 +3,7 @@
 
 
 == The halo model of reionization
-Following @Schneider_2021 @schneider2023cosmologicalforecast21cmpower:
+Following @Schneider_2021 @schneider2023cosmologicalforecast21cmpower, the halo model describes (#link(<backup_full_profiles>, "derivation")):
 #line(length: 100%, stroke: color.white.transparentize(100%))
 #pause
 
@@ -16,7 +16,11 @@ $
 $
   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))
 $
-
+// From the xray emission
+// primordial + heating term
+// expansion + deposition by xrays
+// => xrays are assumed to be the only source of heating
+//
 #pause
 $
   derivative(V_b, t) = dot(N)_"ion"(t) / overline(n)_H^0 - alpha_B dot C / a^3 dot overline(n)_H^0 dot V_b
@@ -26,8 +30,15 @@ $
 // $
 
 #pagebreak()
+Visually:
 
+#image("assets/profiles.png")
+// COMMENTS:
+// - contribution from the lyman lines
+// - 1/r^2 decrease from spreading photons
+// - more steep outwards + sharp drop due to redshifting out of line
 
+#pagebreak()
 
 
 == Revisiting the 21cm signal

implementation.typ

@@ -3,12 +3,37 @@
 #let notebook = json("../workdir/11_visualization/simple_run_example.ipynb")
 
 
-= Implementation
+= Adaptations
+
+
+== Central changes
+
+- profile generation taking into account halo growth rate
+
+- reading merger trees + inferring growth rates
+
+- parallel painting across multiple halo bins
+// important since the bins are more now
+
+- performance and ease of use
+// largely through vectorization -> still "native" python
+// usage of HDF5
+// solid caching mechanisms -> resume simulations, etc...
+
+// #v(5em)
+// #text(
+//   size: .7em,
+// )[
+//   (#link(<backup_validation>, "Validated"))
+// ]
+
+
 == Simplified usage
 
 #text(
-  size: .7em,
+  size: .65em,
 )[
+  #columns(2, gutter: 3pt)[
     #show raw: it => {
       show regex("pin\d"): it => pin(eval(it.text.slice(3)))
       it
@@ -18,6 +43,7 @@
       language: "python",
       code_cell(notebook, cell_id: "code_for_run"),
     )
+  ]
 // #pinit-point-to(1)[Hello]
 // #pinit-point-to(2)[Hello]
 // #pinit-point-to(3)[Hello]
@@ -27,4 +53,3 @@
 ]
 
 
-#link(<backup_validation>, "Validated")

introduction.typ

@@ -9,7 +9,10 @@
 
 - Is strongly linked to the formation and growth of the first galaxies and black holes.
 
-- Sets the stage for many observables: CMB secondary anisotropies, 21-cm signal, high-z galaxy surveys.
+- Sets the stage for many observables:
+  - CMB secondary anisotropies
+  - 21-cm signal
+  - high-z galaxy surveys.
 // reformulate
 
 
@@ -20,12 +23,19 @@ The brigthtness temperature describes the difference between the CMB temperature
 
 #v(1em)
 
-#grid(columns: 2, align: center)[
+#grid(columns: 2, align: center, column-gutter: 1em)[
-  #image("assets/cmb_black_body_spectrum.svg", height: 1fr, fit: "contain")   #text(size: 0.8em)[from @cmb_spectrum]
+  #image("assets/cmb_and_dtb.jpeg", height: 1fr, fit: "contain")   #text(size: 0.8em)[from @cmb_spectrum]
 ][
   #pause
-  Removing the contribution from the black body spectrum of the CMB yields the explicit 21-cm signal:
+  #set text(size: 0.8em)
-  #image("assets/cmb_black_body_spectrum.svg", height: 1fr, fit: "contain")
+  remove contribution from the BB spectrum:
+
+  _differential brightness temperature_
+
+  $==>$ the actual 21-cm signal
+
+  #image("assets/brighness_temperature.png", fit: "contain")
+  from @Schaeffer_2023
 ]
 
 #pagebreak()
@@ -37,6 +47,9 @@ The brigthtness temperature describes the difference between the CMB temperature
   #text(size: 0.8em)[from @Pritchard2012]
 ]
 
+// COMMENTS:
+
+
 
 == Expression the 21-cm signal
 Expressing the _differential brightness temperature_ (e.g @Pritchard2012):
@@ -59,113 +72,37 @@ $ <eq:dTb>
 #layouts.contained(
   [
     *Traditional approaches*
-
+    // From first principles
-    // keypoints that describe heavy hydro + radiative transfer simulations
+    - need to cover large dynamic range
-    - require hydrodynamics
+    // small scales to resolve sources + sinks + feedback
-    - require radiative transfer
+    // large scales to capture statistics
-    - scale poorly
+    - hydrodynamics & radiative transfer
+    - hard to scale
 
     $=>$ no reproducibility
     #pause
   ],
   [
+    #pad(1em)[
+      #align(left)[
         #text(weight: "bold")[semi-numerical approaches]
 
-    such as #beorn @Schaeffer_2023, `21cmFAST` [CITATION]
+        such as #beorn @Schaeffer_2023, `21cmFAST` @21cmfast
-    - approximative treatment
+
-    - link
+        // IF ASKED: difference with `21cmFAST`:
-    - scalable + efficient
+        // based on excursion formalistm -> only valid >= 1Mpc, which is ideal for large volumes + statistics => 21-cm forecasts
+
+        $->$ approximative treatment
+
+        $->$ link
+
+        $->$ scalable + efficient
 
         $=>$ reproducible and flexible
+        // interesting to build emulators for instance
+      ]
+
+    ]
   ]
 )
 
-
-// #layouts.two-boxes(
-//   [
-//     #text(weight: "bold")[Traditional approaches]
-
-//     // keypoints that describe heavy hydro + radiative transfer simulations
-//     - require hydrodynamics
-//     - require radiative transfer
-//     - scale poorly
-
-//     $=>$ no reproducibility
-//     #pause
-//   ],
-//   [
-//     *semi-numerical approaches*
-
-//     such as #beorn @Schaeffer_2023, `21cmFAST` [CITATION]
-//     - approximative treatment
-//     - link
-//     - scalable + efficient
-
-//     $=>$ reproducible and flexible
-
-
-//   ]
-// )
-
-#pagebreak()
-
-== Matrix
-
-#layouts.matrix((
-  brand.wordmark,
-  brand.wordmark,
-  brand.wordmark,
-  brand.wordmark,
-  brand.wordmark,
-  brand.wordmark
-))
-
-== Contained
-#layouts.contained(
-  columns(2, [
-    - #lorem(10)
-    - #lorem(15)
-    - #lorem(25)
-  ]),
-  brand.wordmark
-)
-
-
-
-== Four columns
-
-#layouts.four-columns(
-  [
-    #text(weight: "bold", brand.wordmark)
-    #v(1em)
-    #text(size: 10.5pt)[#lorem(60)]
-  ],
-  [
-    #text(weight: "bold", brand.wordmark)
-    #v(1em)
-    #text(size: 10.5pt)[#lorem(45)]
-  ],
-  [
-    #text(weight: "bold", brand.wordmark)
-    #v(1em)
-    #text(size: 10.5pt)[#lorem(75)]
-  ],
-  [
-    #text(weight: "bold", brand.wordmark)
-    #v(1em)
-    #text(size: 10.5pt)[#lorem(50)]
-  ]
-)
-
-
-
-== Two columns
-
-#layouts.contained(
-  columns(2, [
-    - #lorem(10)
-    - #lorem(15)
-    - #lorem(25)
-  ]),
-  brand.wordmark
-)

main.typ

@@ -107,6 +107,7 @@
     institution: [ETH Zürich, University of Zürich],
     // logo: brand.logo,
   ),
+  config-common(handout: true)
   // footer-left: self => [..#padded_logos],
 )
 
@@ -126,7 +127,7 @@
 = End
 == Thank you for your attention
 
-#bibliography("references.bib")
+#bibliography("references.bib", title: "References")
 #show: appendix
 #include("backup.typ")
 

main2.typ

@@ -1,147 +0,0 @@
-#import "@preview/touying:0.6.1": *
-#import "@preview/touying-unistra-pristine:1.4.2": *
-
-#show: unistra-theme.with(
-  aspect-ratio: "16-9",
-  config-info(
-    title: [Title],
-    author: [Author],
-    date: datetime.today().display("[month repr:long] [day], [year repr:full]"),
-    logo: image("assets/cmb_black_body_spectrum.svg"),
-  ),
-  config-store(
-    quotes: (
-      left: "‘",
-      right: "’",
-    ),
-    icon-links: (
-      "image": (
-        regex("\.(jpg|jpeg|png|bmp|svg|webp|tiff)$"),
-        none,
-      ),
-    ),
-  ),
-)
-
-#title-slide(logo: image("assets/eth-logo.svg"))
-
-= Example Section Title
-
-== Example Slide
-
-A slide with *important information*.
-
-#pause
-
-=== Highlight
-This is #highlight(fill: blue.C)[highlighted in blue]. This is #highlight(fill: yellow.C)[highlighted in yellow]. This is #highlight(fill: green.C)[highlighted in green]. This is #highlight(fill: red.C)[highlighted in red].
-
-#hero(
-  image("assets/eth-logo.svg"),
-  title: "Hero",
-  subtitle: "Subtitle",
-  hide-footer: false,
-)
-
-#hero(
-  image("assets/cmb_black_body_spectrum.svg", width: 100%, height: 100%),
-  txt: (
-    text: "This is an "
-      + highlight(
-        fill: yellow.C,
-      )[RTL#footnote[RTL = right to left. Oh, and here's a footnote!] hero with text and no title]
-      + ".\n",
-    enhanced: false,
-  ),
-  direction: "rtl",
-  footnote: true,
-)
-
-#gallery(
-  // image("../assets/cat1.jpg", width: auto, height: 50%),
-  // image("../assets/cat2.jpg", width: auto, height: 50%),
-  // image("../assets/cat1.jpg", width: auto, height: 50%),
-  // image("../assets/cat2.jpg", width: auto, height: 50%),
-  title: "Gallery",
-  captions: (
-    "Cat 1",
-    "Cat 2",
-    "Cat 1 again",
-    "Cat 2 again",
-  ),
-  columns: 4,
-)
-
-#focus-slide(
-  theme: "smoke",
-  [
-    This is a focus slide \ with theme "smoke"
-  ],
-)
-
-#focus-slide(
-  theme: "neon",
-  icon: nv-icon("text-undo"),
-  [
-    This is a focus slide \ with theme "neon" and Nova icon "text-undo"
-  ],
-)
-
-#focus-slide(
-  theme: "yellow",
-  icon: us-icon("book-open"),
-  [
-    This is a focus slide \ with theme "yellow" and Unistra icon "book-open"
-  ],
-)
-
-#focus-slide(
-  c1: black,
-  c2: white,
-  icon: us-icon("plant"),
-  [
-    This is a focus slide \ with custom colors \ and Unistra icon "plant"
-    \ Next: Section 2
-  ],
-  text-color: yellow.D,
-)
-
-= Section 2
-
-== Hey! New Section!
-
-#lorem(30)
-#pause
-#lorem(20)
-#pause
-Hello!
-=== Heading 3
-
-#lorem(10)
-
-==== Heading 4
-
-#lorem(80)
-
-#quote(
-  attribution: [from the Henry Cary literal translation of 1897 | *Noticed the custom quotes?*],
-)[
-  ... I seem, then, in just this little thing to be wiser than this man at
-  any rate, that what I do not know I do not think I know either.
-]
-
-#slide[
-  First column. #lorem(15)
-][
-  Second column. #lorem(15)
-]
-
-== Icon Links
-
-https://i.edoyen.com/ShareX/2025/07/ky3Hdt.gif
-
-#link("https://i.edoyen.com/ShareX/2025/07/ky3Hdt.gif")[with \#link]
-
-https://i.edoyen.com/ShareX/2025/07/ky3Hdt.gif
-
-https://i.edoyen.com/ShareX/2025/07/ky3Hdt.jpg

references.bib

@@ -441,5 +441,9 @@ archivePrefix = {arXiv},
 
 @website{cmb_spectrum,
    title = "CMB spectrum",
-   url = "https://commons.wikimedia.org/wiki/File:Cmbr.svg",
+   url = "https://asd.gsfc.nasa.gov/archive/arcade/cmb_intensity.html",
 }
+
+
+
+

refinements.typ

@@ -21,7 +21,12 @@
     #pause
   ],
   [
-    ...
+    $->$ inaccurate when applied to all halos
+
+    $->$ #text(weight: "bold")[inconsistent] with the N-body output
+
+    #pause
+    $->$ stochasticity for a more realistic description?
   ]
 )
 
@@ -31,13 +36,41 @@
 
 #image_cell(notebook, cell_id: "profile_plot_alpha_dependence")
 
+$M_"h" = 6.08 dot 10^11 M_dot.circle$ (fixed)
+
+$==>$ correction up to $times 5$
+
+// COMMENTS
+// That will be directly affect the global signal as well
+// shifting
+//
+// Yu-Siu already investigated the more nuanced effect of stochasticity but the approach we propose should supersede that
+
+#pagebreak()
 
 == Inferring growth from #smallcaps[Thesan] data
-#lorem(50)
+- already includes precomputed merger trees @Springel2005
+// ideal for rapid iterations
+
+- follow main progenitor branch back in time
+
+- fit the exponential model to main progrenitor branch
+// in a parallelized fashion => want to stay fast
+// fix the original mass for max. consistency
+// fix the allowed dynamic range
+
+- use *individual growth* to select profile
+// this sort of "breaks the degeneracy" between halos of the same mass but different growth histories
+
+- *self-consistent*#pause$*$#meanwhile treatment of halo growth leveraging the snapshots
+
+
+#pagebreak()
+
 #let notebook = json("../workdir/11_visualization/show_trees.ipynb")
 #[
   #set image(width: 100%, fit: "contain")
   #image_cell(notebook, cell_id: "merger_tree_and_fitting")
 ]
-
+// COMMENTS:
-
+// no clear trend between mass and growth rate

results.typ

@@ -4,10 +4,44 @@
 == Map outputs
 #let notebook = json("../workdir/11_visualization/simulation_maps.ipynb")
 
+#grid(
+  columns: (auto, 10em)
+)[
   #image_cell(notebook, cell_id: "presentation_x_alpha_map")
+][
+  #lorem(20)
+]
+
+#pagebreak()
+
+#grid(
+  columns: (auto, 10em)
+)[
   #image_cell(notebook, cell_id: "presentation_temperature_map")
+][
+  #lorem(20)
+]
+
+#pagebreak()
+
+#grid(
+  columns: (auto, 10em)
+)[
   #image_cell(notebook, cell_id: "presentation_xHII_map")
+][
+  #lorem(20)
+]
+
+#pagebreak()
+
+#grid(
+  columns: (auto, 10em)
+)[
   #image_cell(notebook, cell_id: "presentation_dtb_map")
+][
+  #lorem(20)
+]
+