add organic-molecule.typ and branch-cuts-2.typ converted from Latex and add 3d shading via radial gradient to assets/sublattice-points/sublattice-points.typ

Author: janosh

assets/branch-cuts-2/branch-cuts-2.typ

@@ -0,0 +1,94 @@
+#import "@preview/cetz:0.3.4": canvas, draw
+#import draw: line, content, bezier
+
+#set page(width: auto, height: auto, margin: 8pt)
+
+// Functions for the branch cuts - adjusted to better match the original
+// Increased vertical scaling to spread the curves further apart
+#let f1(x) = 5 / (calc.sqrt(x) + 2)
+#let f2(x) = 5 * (1 / (x + 2) + 1 / 3)
+#let f3(x) = -5 / (calc.sqrt(x) + 2)
+#let f4(x) = -5 * (1 / (x + 2) + 1 / 3)
+
+#canvas({
+  // Set up the coordinate system
+  let (width, height) = (10, 8)
+
+  // Draw axes
+  line(
+    (0, 0),
+    (width, 0),
+    mark: (end: "stealth", fill: black),
+    stroke: 1.2pt,
+    name: "x-axis",
+  )
+  content((rel: (0, -0.2), to: "x-axis.end"), $"Re"(q_0)$, anchor: "north-east")
+
+  line(
+    (0, -height / 2),
+    (0, height / 2),
+    mark: (end: "stealth", fill: black),
+    stroke: 1.2pt,
+    name: "y-axis",
+  )
+  content((rel: (0.2, 0), to: "y-axis.end"), $"Im"(q_0)$, anchor: "north-west")
+
+  // Draw the curves
+  // Helper function to draw a parametric curve
+  let draw-curve(f, domain: (1, 9), samples: 100, stroke: black) = {
+    let points = ()
+    let step = (domain.at(1) - domain.at(0)) / samples
+
+    for i in range(samples + 1) {
+      let x = domain.at(0) + i * step
+      let y = f(x)
+      points.push((x, y))
+    }
+
+    for i in range(samples) {
+      line(
+        points.at(i),
+        points.at(i + 1),
+        stroke: stroke,
+      )
+    }
+  }
+
+  // Draw the red curves
+  draw-curve(f1, stroke: red + 2pt)
+  draw-curve(f2, stroke: red + 2pt)
+
+  // Draw the blue curves
+  draw-curve(f3, stroke: blue + 2pt)
+  draw-curve(f4, stroke: blue + 2pt)
+
+  // Calculate points on the curves for arrow start positions
+  let top_red_x = 4
+  let top_red_y = f2(top_red_x) // Use the second red curve (higher one)
+
+  let bottom_blue_x = 4
+  let bottom_blue_y = f4(bottom_blue_x) // Use the fourth curve (lower blue one)
+
+  // Add the dashed arrows pointing to the origin
+  // First arrow (from top red curve to origin) - flipped curve direction
+  bezier(
+    (top_red_x, top_red_y), // start point - on the red curve
+    (3.5, 0), // end point - at the origin
+    (3.6, top_red_y * 0.7), // control point - flipped direction
+    stroke: (dash: "dashed", thickness: 1pt),
+    mark: (end: "stealth", fill: black, scale: 0.8),
+    name: "arrow1",
+  )
+  content((rel: (0.15, 0), to: "arrow1.80%"), $k arrow.r 0$, anchor: "west")
+
+  // Second arrow (from bottom blue curve to origin) - flipped curve direction
+  bezier(
+    (bottom_blue_x, bottom_blue_y), // start point - on the lower blue curve
+    (3.5, 0), // end point - at the origin
+    (3.6, bottom_blue_y * 0.7), // control point - flipped direction
+    stroke: (dash: "dashed", thickness: 1pt),
+    mark: (end: "stealth", fill: black, scale: 0.8),
+    name: "arrow2",
+  )
+  content((rel: (-0.15, 0), to: "arrow2.80%"), $k arrow.r 0$, anchor: "east")
+})

assets/organic-molecule/organic-molecule.typ

@@ -0,0 +1,228 @@
+#import "@preview/cetz:0.3.4": canvas, draw
+#import draw: circle, content, line, on-layer
+
+#set page(width: auto, height: auto, margin: 5pt)
+
+// Atom with 3D shading effect
+#let atom(pos, color, element, radius: 0.3, name: none) = {
+  // Base circle with main color
+  circle(
+    pos,
+    radius: radius,
+    stroke: none,
+    fill: color,
+    name: name,
+  )
+
+  // Gradient overlay for 3D effect
+  circle(
+    pos,
+    radius: radius,
+    stroke: none,
+    fill: gradient.radial(
+      color.lighten(85%),
+      color,
+      color.darken(25%),
+      focal-center: (25%, 20%),
+      focal-radius: 10%,
+      center: (30%, 25%),
+    ),
+  )
+
+  // Add element label
+  let text-color = if color == rgb("#333333") { white } else { black }
+
+  // Calculate text size based on radius
+  let text-size = if radius < 0.4 { 10pt } else { 14pt }
+
+  content(
+    pos,
+    text(fill: text-color, weight: "bold", size: text-size)[#element],
+    anchor: "center",
+  )
+}
+
+#canvas({
+  // Define atom colors
+  let hydrogen-color = rgb("#eee")
+  let carbon-color = rgb("#333")
+  let nitrogen-color = rgb("#3333cc")
+  let oxygen-color = red.darken(10%)
+
+  // Define atom sizes - increased to match target image
+  let h-radius = 0.35
+  let heavy-radius = 0.5
+
+  // Adjust hydrogen positions to be further from connected atoms
+  // Original positions from LaTeX
+  let orig-h-positions = (
+    ("H1", (-2.9, 1.39)),
+    ("H2", (-3.5, 1.23)),
+    ("H3", (-3.8, 0.15)),
+    ("H4", (-1.7, -0.6)),
+    ("H5", (-0.3, 1.4)),
+    ("H6", (-1, 1.15)),
+    ("H7", (0, -0.7)),
+    ("H8", (1, -1.82)),
+    ("H9", (0.2, -1.8)),
+    ("H10", (3.5, 0.5)),
+  )
+
+  // Heavy atom positions
+  let c-positions = (
+    ("C1", (-3.19, 0.68)),
+    ("C2", (-0.78, 0.67)),
+    ("C3", (0.47, -0.18)),
+    ("C4", (1.73, 0.67)),
+  )
+
+  let n-positions = (
+    ("N1", (-2.00, -0.15)),
+    ("N2", (0.51, -1.32)),
+  )
+
+  let o-positions = (
+    ("O1", (1.80, 1.88)),
+    ("O2", (2.86, -0.07)),
+  )
+
+  // Function to move hydrogen atoms further from their connected atoms
+  let adjust-h-position(h-pos, connected-pos, factor: 1.5) = {
+    let (hx, hy) = h-pos
+    let (cx, cy) = connected-pos
+    let dx = hx - cx
+    let dy = hy - cy
+    let dist = calc.sqrt(dx * dx + dy * dy)
+    let new-dist = dist * factor
+    let scale = new-dist / dist
+    (cx + dx * scale, cy + dy * scale)
+  }
+
+  // Connection map: which hydrogen connects to which heavy atom
+  let h-connections = (
+    "H1": "C1",
+    "H2": "C1",
+    "H3": "C1",
+    "H4": "N1",
+    "H5": "C2",
+    "H6": "C2",
+    "H7": "C3",
+    "H8": "N2",
+    "H9": "N2",
+    "H10": "O2",
+  )
+
+  // Combine all heavy atom positions for lookup
+  let heavy-atoms = (:)
+  for (name, pos) in c-positions { heavy-atoms.insert(name, pos) }
+  for (name, pos) in n-positions { heavy-atoms.insert(name, pos) }
+  for (name, pos) in o-positions { heavy-atoms.insert(name, pos) }
+
+  // Adjust hydrogen positions
+  let h-positions = (:)
+  for (name, pos) in orig-h-positions {
+    let connected-atom = h-connections.at(name)
+    let connected-pos = heavy-atoms.at(connected-atom)
+    h-positions.insert(name, adjust-h-position(pos, connected-pos))
+  }
+
+  // Further adjust overlapping hydrogens
+  // Adjust H1 and H2 which overlap in the top left
+  let h1-pos = h-positions.at("H1")
+  let h2-pos = h-positions.at("H2")
+  h-positions.insert("H1", (h1-pos.at(0) - 0.2, h1-pos.at(1) + 0.2))
+  h-positions.insert("H2", (h2-pos.at(0) - 0.2, h2-pos.at(1) - 0.2))
+
+  // Adjust H8 and H9 which overlap near the right N atom
+  let h8-pos = h-positions.at("H8")
+  let h9-pos = h-positions.at("H9")
+  h-positions.insert("H8", (h8-pos.at(0) + 0.3, h8-pos.at(1) - 0.2))
+  h-positions.insert("H9", (h9-pos.at(0) - 0.3, h9-pos.at(1) - 0.2))
+
+  // Draw all atoms
+  // Draw carbon atoms
+  for (name, pos) in c-positions {
+    atom(pos, carbon-color, "C", radius: heavy-radius, name: name)
+  }
+
+  // Draw nitrogen atoms
+  for (name, pos) in n-positions {
+    atom(pos, nitrogen-color, "N", radius: heavy-radius, name: name)
+  }
+
+  // Draw oxygen atoms
+  for (name, pos) in o-positions {
+    atom(pos, oxygen-color, "O", radius: heavy-radius, name: name)
+  }
+
+  // Draw hydrogen atoms
+  for (name, pos) in h-positions {
+    atom(pos, hydrogen-color, "H", radius: h-radius, name: name)
+  }
+
+  // Draw bonds on a background layer (behind atoms)
+  on-layer(
+    -1,
+    {
+      // Main chain
+      let bond-chain = ("H1", "C1", "N1", "C2", "C3", "C4", "O1")
+      for i in range(bond-chain.len() - 1) {
+        let from = bond-chain.at(i)
+        let to = bond-chain.at(i + 1)
+
+        let from-pos = if from.starts-with("H") {
+          h-positions.at(from)
+        } else {
+          heavy-atoms.at(from)
+        }
+
+        let to-pos = if to.starts-with("H") {
+          h-positions.at(to)
+        } else {
+          heavy-atoms.at(to)
+        }
+
+        line(
+          from-pos,
+          to-pos,
+          stroke: (paint: gray, thickness: 3.5pt),
+        )
+      }
+
+      // Additional bonds
+      let additional-bonds = (
+        ("H2", "C1"),
+        ("H3", "C1"),
+        ("N1", "H4"),
+        ("C2", "H5"),
+        ("C2", "H6"),
+        ("C3", "H7"),
+        ("C3", "N2"),
+        ("N2", "H8"),
+        ("N2", "H9"),
+        ("C4", "O2"),
+        ("O2", "H10"),
+      )
+
+      for (from, to) in additional-bonds {
+        let from-pos = if from.starts-with("H") {
+          h-positions.at(from)
+        } else {
+          heavy-atoms.at(from)
+        }
+
+        let to-pos = if to.starts-with("H") {
+          h-positions.at(to)
+        } else {
+          heavy-atoms.at(to)
+        }
+
+        line(
+          from-pos,
+          to-pos,
+          stroke: (paint: gray, thickness: 3.5pt),
+        )
+      }
+    },
+  )
+})

assets/sublattice-points/sublattice-points.typ

@@ -3,6 +3,24 @@
 
 #set page(width: auto, height: auto, margin: 8pt)
 
+// Atom with 3D shading effect
+#let shaded-circle(pos, color, radius: 0.1, name: none, stroke: 0.2pt) = {
+  circle(
+    pos,
+    radius: radius,
+    stroke: stroke,
+    fill: gradient.radial(
+      color.lighten(85%),
+      color,
+      color.darken(25%),
+      focal-center: (25%, 20%),
+      focal-radius: 10%,
+      center: (30%, 25%),
+    ),
+    name: name,
+  )
+}
+
 #canvas({
   // Define styles and constants
   let grid-size = 2 // number of points in each direction
@@ -29,11 +47,12 @@
       // Use modulo to cycle through colors
       let color-idx = calc.rem(ii - 2 * jj, colors.len())
       if color-idx < 0 { color-idx += colors.len() }
-      circle(
+
+      // Use the shaded-circle function instead of regular circle
+      shaded-circle(
         (x, y),
+        colors.at(color-idx),
         radius: dot-radius * 1.2,
-        fill: colors.at(color-idx),
-        stroke: .5pt,
         name: str(ii) + "," + str(jj),
       )
     }