starting to take shape

backup.typ

@@ -1,6 +1,4 @@
-#import "importer/main.typ": *
+#import "globals.typ": *
-#import "@preview/physica:0.9.5": *
-
 
 
 == Validation <backup_validation>

beorn.typ

@@ -0,0 +1,116 @@
+#import "globals.typ": *
+
+= #beorn
+
+
+== Procedure
+
+#let notebook = json("../workdir/11_visualization/simplified_visualization_of_procedure.ipynb")
+
+#grid(
+  columns: (auto, 5em, auto, 5em, auto),
+  rows: (60%, auto),
+  align: center,
+  row-gutter: 2em,
+  image_cell(notebook, cell_id: "step_profile_1d"),
+  [#pin(1)$==>$#pin(2)],
+  image_cell(notebook, cell_id: "step_kernel_3d"),
+  [#pin(3)$==>$#pin(4)],
+  image_cell(notebook, cell_id: "step_profile_3d"),
+
+  [
+   1-d profile
+  ],
+  [],
+  [
+   3-d kernel
+
+   (localized)
+  ],
+  [],
+  [
+   3-d contribution on a grid
+  ],
+)
+
+
+#pause
+#pinit-point-to(
+  (1, 2),
+  pin-dx: 20pt,
+  pin-dy: -20pt,
+  body-dx: -70pt,
+  body-dy: -80pt,
+  offset-dx: 20pt,
+  offset-dy: 30pt,
+)[spherical symmetry]
+
+
+#pause
+#pinit-point-to(
+  (3, 4),
+  pin-dx: 20pt,
+  pin-dy: -20pt,
+  body-dx: -90pt,
+  body-dy: -80pt,
+  offset-dx: 20pt,
+  offset-dy: 30pt,
+)[convolution (fft)]
+
+
+#pagebreak()
+
+
+#grid(
+  columns: (auto, 8em, auto),
+  rows: (38%, 1em, 38%),
+  align: center,
+  column-gutter: 2em,
+  row-gutter: 0.3em,
+
+  image_cell(notebook, cell_id: "step_profile_3d"),
+  grid.cell(
+    rowspan: 3,
+    image_cell(notebook, cell_id: "step_profile_3d_overlap"),
+  ),
+  [],
+  // [],
+  // [],
+
+  [#h(3em) Multiple contributions $==>$],
+  [
+    $==>$ _Postprocessing_
+
+    (overlaps, normalization, ...)
+  ],
+  // [],
+  // [],
+
+  image_cell(notebook, cell_id: "step_profile_3d_second"),
+  [],
+  // [],
+  // [],
+)
+#pagebreak()
+
+== Postprocessing
+- ionization overlaps
+- corrections due to RSD
+- computation of derived quantities
+- summary statistics
+
+
+== Maps
+Through the redshifting of photons, the brightness temperature across redshift slices will be measured in a frequency band
+
+$=>$ representation as a lightcone
+#align(center)[
+  #image("assets/lightcone.png")
+]
+from @Schaeffer_2023
+
+== Signal
+#align(center)[
+  #image("assets/signals.png")
+]
+from @Schaeffer_2023

conclusion.typ

@@ -0,0 +1,15 @@
+#import "globals.typ": *
+
+= Conclusion
+== Summary
+- We presented Beorn, a new code to simulate the 21cm signal from the EoR and Cosmic Dawn.
+- 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.
+- We validated Beorn against numerical simulations and showed that it can reproduce their results with good accuracy.
+- Beorn is publicly available and can be used for a variety of applications, including forecasting, parameter estimation, and data analysis.
+
+== Upcoming improvements
+- investigation + parameterization of stochasticity
+- application to larger volumes
+- fully parallel runs
+

globals.typ

@@ -0,0 +1,12 @@
+#import "importer/main.typ": *
+#import "@preview/physica:0.9.5": *
+#import "@preview/touying:0.6.1": *
+#import "@preview/pinit:0.2.2": *
+
+#import "lineal/lib.typ": *
+
+#show math.equation: set align(center)
+#show image: set align(center)
+
+
+#let beorn = raw("BEoRN")

halo_model.typ

@@ -0,0 +1,52 @@
+#import "globals.typ": *
+
+
+
+== The halo model of reionization
+Following @Schneider_2021 @schneider2023cosmologicalforecast21cmpower:
+#line(length: 100%, stroke: color.white.transparentize(100%))
+#pause
+
+$
+  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)
+$
+
+#pause
+
+$
+  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))
+$
+
+#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
+$
+// $
+//   x_("HII")(r bar M, z) = theta_"H" lr([R_b (M, z) - r], size: #150%)
+// $
+
+#pagebreak()
+
+
+
+
+== Revisiting the 21cm signal
+$
+  d T_"b" (bold(x), z) tilde.eq T_0 (z) dot
+  #pin(1) x_"HI" (bold(x), z) #pin(2) dot
+  (1 + delta_b (bold(x), z)) dot
+  (x_alpha (bold(x), z)) / (#pin(3)  1 + x_alpha (bold(x), z) #pin(4) ) dot
+  ((1 - T_"CMB" (z)) / (#pin(5) T_"gas" (bold(x), z) #pin(6)))
+$ <eq:dTb>
+
+#pause
+// #pinit-highlight(1, 20)
+#pinit-point-from((1, 2))[from $x_"HII"$]
+#pause
+
+#pinit-point-from((3, 4))[From $rho_alpha$]
+#pause
+
+#pinit-point-from((5, 6))[From $rho_"h"$]
+
+#pagebreak()

implementation.typ

@@ -1,16 +1,30 @@
-#import "importer/main.typ": *
+#import "globals.typ": *
 
 #let notebook = json("../workdir/11_visualization/simple_run_example.ipynb")
-#show raw: it => {
+
-  show regex("pin\d"): it => pin(eval(it.text.slice(3)))
-  it
-}
 
 = Implementation
 == Simplified usage
 
+#text(
+  size: .7em,
+)[
+  #show raw: it => {
+    show regex("pin\d"): it => pin(eval(it.text.slice(3)))
+    it
+  }
+  #code-block(
+    filename: "beorn.py",
+    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]
+// #pinit-point-to(4)[Hello]
+// #pinit-point-to(5)[Hello]
+
+]
 
 
-#code_cell(notebook, cell_id: "code_for_run")
+#link(<backup_validation>, "Validated")
-
-

introduction.typ

@@ -1,6 +1,4 @@
-#import "importer/main.typ": *
+#import "globals.typ": *
-#import "@preview/physica:0.9.5": *
-#import "@preview/touying:0.6.1": *
 
 
 = Simulating the Epoch of Reionization
@@ -14,67 +12,160 @@
 - Sets the stage for many observables: CMB secondary anisotropies, 21-cm signal, high-z galaxy surveys.
 // reformulate
 
-== The 21cm signal
+
+== The 21-cm signal
+
 
 The brigthtness temperature describes the difference between the CMB temperature and the spin temperature of neutral hydrogen
-#grid[
+
-  #image("assets/cmb_black_body_spectrum.svg", height: 1fr, fit: "contain") @cmb_spectrum
+#v(1em)
+
+#grid(columns: 2, align: center)[
+  #image("assets/cmb_black_body_spectrum.svg", 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:
   #image("assets/cmb_black_body_spectrum.svg", height: 1fr, fit: "contain")
-
 ]
 
+#pagebreak()
+
 
 
 #align(center)[
-  #image("assets/evolution_of_dtb.png", fit: "contain")
+  #image("assets/evolution_of_dtb.png", height: 85%, fit: "contain")
+  #text(size: 0.8em)[from @Pritchard2012]
 ]
-@Pritchard2012
 
-#pagebreak()
+
+== Expression the 21-cm signal
+Expressing the _differential brightness temperature_ (e.g @Pritchard2012):
 
 $
-  d T_"b" (bold(x), z) tilde.eq T_0 (z) dot x_"HI" (bold(x), z)  dot (1 + delta_b (bold(x), z)) dot (x_alpha (bold(x), z)) / (1 + x_alpha (bold(x), z) ) dot ((1 - T_"CMB" (z)) / (T_"gas" (bold(x), z)))
+  d T_"b" (bold(x), z) tilde.eq T_0 (z) dot
+  #pin(1) x_"HI" (bold(x), z) #pin(2) dot
+  (1 + delta_b (bold(x), z)) dot
+  (x_alpha (bold(x), z)) / (#pin(3)  1 + x_alpha (bold(x), z) #pin(4) ) dot
+  ((1 - T_"CMB" (z)) / (#pin(5) T_"gas" (bold(x), z) #pin(6)))
 $ <eq:dTb>
-(e.g @Pritchard2012)
-
-
-
-== The halo model of reionization
-
-
-
-Following @Schneider_2021 @schneider2023cosmologicalforecast21cmpower:
-
-$
-  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)
-$
-#line(
-  length: 100%
-)
-$
-  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))
-$
-#line(
-  length: 100%
-)
-$
-  x_("HII")(r bar M, z) = theta_"H" lr([R_b (M, z) - r], size: #150%)
-$
 
+// Explanation
+- further modulation by _RSD_
 
 
 == The current state of simulations
-#lorem(20)
-
-- slow and big
-- radiative transfer // what are the downsides
 
 
-$==>$ semi-numerical approaches such as `BEoRN` @Schaeffer_2023
+#layouts.contained(
+  [
+    *Traditional approaches*
+
+    // keypoints that describe heavy hydro + radiative transfer simulations
+    - require hydrodynamics
+    - require radiative transfer
+    - scale poorly
+
+    $=>$ no reproducibility
+    #pause
+  ],
+  [
+    #text(weight: "bold")[semi-numerical approaches]
+
+    such as #beorn @Schaeffer_2023, `21cmFAST` [CITATION]
+    - approximative treatment
+    - link
+    - scalable + efficient
+
+    $=>$ reproducible and flexible
+  ]
+)
 
 
-#link(<backup_validation>, "validation")
+// #layouts.two-boxes(
+//   [
+//     #text(weight: "bold")[Traditional approaches]
 
-== `BEoRN`
+//     // 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

@@ -1,8 +1,6 @@
-#import "@preview/diatypst:0.7.0": *
+#import "globals.typ": *
-#import "importer/main.typ": *
+
-#import "@preview/physica:0.9.5": *
 
-// Patch the ETH logo to actually be white:
 #let logo = "assets/uzh-logo.svg"
 #let original = read(logo)
 #let changed = original.replace(
@@ -26,122 +24,109 @@
 #let title-color = color.blue.darken(50%);
 #let bg-color = color.white;
 
+#let padded_logos = logos.map(logo => box(height: 1.5em, inset: (x:0.3cm), logo))
 
 
 ///// Front page /////
 #let notebook = json("../workdir/11_visualization/very_high_res_snapshot.ipynb")
 #let front_image = image_cell(notebook, cell_id: "very_high_res_slice")
-#let (height, space) = layouts.at(layout_size)
+// #title-slide[
-#let width = ratio * height
 
-#set page(
+//   #let space = 2cm
-  height: height,
+//   #place[
-  width: width,
+//     #front_image,
-  footer: none,
+//   ]
-  header: none,
+//   #place[
-  margin: 0cm
+//     #box(
-)
+//       width: 100%,
+//       height: 100%,
+//       fill: color.black.transparentize(65%)
+//     )
+//   ]
 
-#let space = 2cm
+//   #block(
-#place[
+//     inset: (x:0.5*space, y:1em),
-  #set image(
+//     width: 100%,
-    width: 105%,
+//     height: 60%,
-  )
+//     align(bottom)[#text(2.0em, weight: "bold", fill: bg-color, title)],
-  #front_image,
+//     above: 0cm,
-]
+//     below: 0cm,
-#place[
+//   )
-  #box(
-    width: 100%,
-    height: 100%,
-    fill: color.black.transparentize(65%)
-  )
-]
-
-#block(
-  inset: (x:0.5*space, y:1em),
-  width: 100%,
-  height: 60%,
-  align(bottom)[#text(2.0em, weight: "bold", fill: bg-color, title)],
-  above: 0cm,
-  below: 0cm,
-)
 
 
-#let padded_logos = logos.map(logo => box(height: 1.5em, inset: (x:0.3cm), logo))
 
 
-#block(
+//   #block(
-  height: 40%,
+//     height: 40%,
-  width: 100%,
+//     width: 100%,
-  fill: bg-color,
+//     fill: bg-color,
-  inset: (x:0.5*space,top:1cm, bottom: 1em),
+//     inset: (x:0.5*space,top:1cm, bottom: 1em),
-  above: 0cm,
+//     above: 0cm,
-  below: 0cm,
+//     below: 0cm,
-  if subtitle != none {[
+//     if subtitle != none {[
-    #text(1.4em, fill: title-color, weight: "bold", subtitle)
+//       #text(1.4em, fill: title-color, weight: "bold", subtitle)
-  ]} +
+//     ]} +
-  if subtitle != none and date != none { text(1.4em)[ \ ] } +
+//     if subtitle != none and date != none { text(1.4em)[ \ ] } +
-  if date != none {text(1.1em, date)} +
+//     if date != none {text(1.1em, date)} +
-  align(
+//     align(
-    bottom,
+//       bottom,
-    stack(
+//       stack(
-      dir: ltr,
+//         dir: ltr,
-        authors.join(", ", last: " & "),
+//           authors.join(", ", last: " & "),
-        h(1fr),
+//           h(1fr),
-        ..padded_logos,
+//           ..padded_logos,
-    )
+//       )
-  )
+//     )
-)
+//   )
+// ]
+// #slide[
 
+//   // #set page(
+//   //   footer: none,
+//   //   header: none,
+//   //   margin: 0cm
+//   // )
+
+
+// ]
 
 ///// Main content /////
 
-#show: slides.with(
+
-  title: title,
+
-  subtitle: subtitle,
+
-  date: date,
+
-  authors: authors,
+#show: lineal-theme.with(
-  toc: false,
+  aspect-ratio: "16-9",
-  layout: layout_size,
+  // config-common(handout: true),
-  ratio: ratio,
+  config-info(
-  title-color: title-color,
+    title: [#title],
-  bg-color: bg-color,
+    subtitle: [#subtitle],
-  footer-title: footer-title,
+    author: [Author],
-  count: "number"
+    date: datetime.today(),
+    institution: [ETH Zürich, University of Zürich],
+    // logo: brand.logo,
+  ),
+  // footer-left: self => [..#padded_logos],
 )
 
-
+#title-slide()
-
-#show footnote.entry: set text(size: 0.6em)
-#set footnote.entry(gap: 3pt)
-#set align(horizon)
-#set grid(
-  columns: 2,
-  gutter: 2em,
-)
-
-
 
 #include "introduction.typ"
-
+#include "halo_model.typ"
+#include "beorn.typ"
 #include "refinements.typ"
 
 #include "implementation.typ"
 
 #include "results.typ"
+#include "conclusion.typ"
 
 
-
+= End
-#set heading(numbering: none, outlined: false)
+== Thank you for your attention
-= Thank you for your attention
 
 #bibliography("references.bib")
-
+#show: appendix
-// #context let last_page = counter(page).get()
-// #let last_page = counter("page").get()
-// #let last_page = 20
-// freeze the page counter here
-
 #include("backup.typ")
 
-// #counter(page).update(last_page)

refinements.typ

@@ -1,10 +1,36 @@
-#import "importer/main.typ": *
+#import "globals.typ": *
 
 
-= Halo mass history
+= Halo growth
+
+== Motivation
+#layouts.contained(
+  [
+    Crucial dependence on the *star formation rate*
+
+    - assumed to be directly linked to halo growth rate $dot(M)$:
+    $
+      dot(M)_star = f_star (M_"h") dot dot(M_"h")
+
+    $
+    - growth according to the exponential model:
+    $
+      M_"h" (z) = M_"h" (z_0) dot exp[-alpha (z - z_0)]
+    $
+    with $alpha = dot(M_"h")/M_"h"$ the _specific growth rate_
+    #pause
+  ],
+  [
+    ...
+  ]
+)
+
 
 == Effect on the flux profiles
-#lorem(50)
+#let notebook = json("../workdir/11_visualization/alpha_dependence_of_profiles.ipynb")
+
+#image_cell(notebook, cell_id: "profile_plot_alpha_dependence")
+
 
 == Inferring growth from #smallcaps[Thesan] data
 #lorem(50)
@@ -13,3 +39,5 @@
   #set image(width: 100%, fit: "contain")
   #image_cell(notebook, cell_id: "merger_tree_and_fitting")
 ]
+
+

results.typ

@@ -1,6 +1,4 @@
-#import "importer/main.typ": *
+#import "globals.typ": *
-#import "@preview/physica:0.9.5": *
-
 
 = Results
 == Map outputs