Materials Informatics
Structure-based materials informatics workflow. Inspired by fig. 1 in https://doi.org/10.1016/j.cpc.2019.106949.
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materials-informatics.tex (81 lines)
\documentclass[tikz]{standalone}
\usetikzlibrary{positioning, arrows.meta, calc}
\begin{document}
\begin{tikzpicture}[
neuron/.style={circle,fill=black!25,minimum size=20,inner sep=0},
label/.style={font=\large\bfseries, minimum size=3em},
arrow/.style={>={LaTeX[width=5mm,length=5mm]}, ->, line width=1ex, gray, shorten <=1em, shorten >=1em},
]
\begin{scope}[local bounding box=struct]
\node[ball color=black!75, circle, white, scale=1.3] (C1) at (0, 0) {C};
\node[ball color=black!75, circle, white, scale=1.3] (C2) at (0, -1.5) {C};
\node[ball color=blue!75, circle, scale=1.3] (N1) at (-0.5, 1.5) {N};
\node[ball color=red!75, circle, scale=1.3] (O1) at (1.8, 0.5) {O};
\node[ball color=white, circle] (H1) at (1.5, -2.5) {H};
\node[ball color=white, circle] (H2) at (0, -3) {H};
\node[ball color=white, circle] (H3) at (-1.5, -2.5) {H};
\node[ball color=white, circle] (H4) at (-2, 0.75) {H};
\node[ball color=white, circle] (H5) at (1, 2) {H};
\draw[gray, line width=1mm] (H1) -- (C2) -- (C1) -- (N1) (C1) -- (O1) (H2) -- (C2) (H3) -- (C2) (N1) -- (H4) (N1) -- (H5);
\end{scope}
% \draw[rounded corners=1em, thick] (current bounding box.south west)++(-1,-1) rectangle (current bounding box.north east);
\node[label] at (0,-4.5) (structure) {Molecular Structure\vphantom{p}};
\node[label, right=4.5cm of structure] (descriptor) {Descriptor};
\node[label, right=6cm of descriptor] (model) {Model};
\node[label, right=4.5cm of model] (property) {Property};
\node[scale=7, above=1.8cm of property] (alpha) {$\alpha$};
\begin{scope}[shift={($(struct.east)+(2.5,0)$)}, scale=0.6, local bounding box=desc]
\foreach \y [count=\n] in {
{74,25,39,20,3,3,3,3,3},
{25,53,31,17,7,7,2,3,2},
{39,31,37,24,3,3,3,3,3},
{20,17,24,37,2,2,6,5,5},
{3,7,3,2,0,1,0,0,0},
{3,7,3,2,1,0,0,0,0},
{3,2,3,6,0,0,0,1,1},
{3,3,3,5,0,0,1,0,1},
{3,2,3,5,0,0,1,1,0},
} {
\foreach \x [count=\m] in \y {
\node[fill=yellow!\x!purple, minimum size=6mm, text=white] at (\m,5-\n) {\x};
}
}
\end{scope}
\begin{scope}[shift={($(desc.east)+(3,2.5)$)}, local bounding box=mod]
\def\layersep{2.5}
% Input layer
\foreach \y in {1,2,3}
\node[neuron, fill=teal!60] (i\y) at (0,-\y-0.5) {$i\y$};
% Hidden layer
\foreach \y in {1,...,4}
\path node[neuron, fill=blue!50] (h\y) at (\layersep,-\y) {$h\y$};
% Output node
\node[neuron, fill=orange!60] (o) at (2*\layersep,-2.5) {$o$};
% Connect every node in the input layer with every node in the hidden layer.
\foreach \source in {1,2,3}
\foreach \dest in {1,...,4}
\path (i\source) edge (h\dest);
% Connect every node in the hidden layer with the output layer
\foreach \source in {1,...,4}
\path (h\source) edge (o);
\end{scope}
\draw[arrow] (struct.east) -- ++(2.5,0);
\draw[arrow] (desc.east) -- ++(2.5,0);
\draw[arrow] (mod.east) -- ++(2.5,0);
\end{tikzpicture}
\end{document}
Typst
materials-informatics.typ (347 lines)
#import "@preview/cetz:0.3.4": canvas, draw
#import draw: line, content, rect, circle
#set page(width: auto, height: auto, margin: 5pt)
#let neuron(pos, fill: white, text: none, name: none) = {
draw.content(
pos,
text,
frame: "circle",
fill: fill,
stroke: none,
padding: 4pt,
name: name,
)
}
#let atom(pos, element, color: white, text-color: black, padding: 6pt, name: none) = {
// Calculate the radius based on padding to match the original size
let radius = padding + 7pt // Approximation of text size + padding
// Draw base circle with the main color
circle(
pos,
radius: radius,
stroke: none,
fill: color,
)
// Draw gradient overlay for 3D shading effect
circle(
pos,
radius: radius,
stroke: none,
fill: gradient.radial(
color.lighten(75%),
color,
color.darken(15%),
focal-center: (30%, 25%),
focal-radius: 5%,
center: (35%, 30%),
),
)
// Draw the element text on top
content(
pos,
text(fill: text-color, weight: "bold", size: 14pt)[#element],
anchor: "center",
name: name,
)
}
#canvas({
// Define styles
let arrow-style = (
stroke: rgb("#888") + 5pt,
mark: (end: "stealth", size: 15pt),
)
// Set vertical center point for all elements
let vertical-center = 0
// Define spacing constants
let struct-desc-spacing = 2.5 // Closer spacing between structure and descriptor
let model-prop-spacing = 2.5 // Closer spacing between model and property
let component-spacing = 3.5 // Spacing between other components
let label-offset = 4 // Vertical distance from components to labels
let label-y = vertical-center - label-offset // Fixed y-position for all labels
// Define vertical offsets
let molecule-y-offset = 0.5 // Move molecule up
let matrix-y-offset = 0.3 // Move matrix up
// Define component positions
let struct-x = -5.5
let struct-y = vertical-center + molecule-y-offset
let struct-origin = (struct-x, struct-y)
// Draw molecular structure
// Bonds first (so atoms appear on top)
line(
(rel: (1.5, -2.5), to: struct-origin),
(rel: (0, -1.5), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond1",
)
line(
(rel: (0, -1.5), to: struct-origin),
struct-origin,
stroke: rgb("#888") + 3pt,
name: "bond2",
)
line(
struct-origin,
(rel: (-0.5, 1.5), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond3",
)
line(
struct-origin,
(rel: (1.8, 0.5), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond4",
)
line(
(rel: (0, -3), to: struct-origin),
(rel: (0, -1.5), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond5",
)
line(
(rel: (-1.5, -2.5), to: struct-origin),
(rel: (0, -1.5), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond6",
)
line(
(rel: (-0.5, 1.5), to: struct-origin),
(rel: (-2, 0.75), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond7",
)
line(
(rel: (-0.5, 1.5), to: struct-origin),
(rel: (1, 2), to: struct-origin),
stroke: rgb("#888") + 3pt,
name: "bond8",
)
// Now draw atoms on top of bonds - with increased size
// Carbon atoms
atom(struct-origin, "C", color: rgb("#404040"), text-color: white, name: "C1", padding: 5pt)
atom((rel: (0, -1.5), to: struct-origin), "C", color: rgb("#404040"), text-color: white, name: "C2", padding: 5pt)
// Nitrogen atom
atom((rel: (-0.5, 1.5), to: struct-origin), "N", color: rgb("#4444ff"), name: "N1", padding: 6pt)
// Oxygen atom
atom((rel: (1.8, 0.5), to: struct-origin), "O", color: rgb("#ff4444"), name: "O1", padding: 7pt)
// Hydrogen atoms
atom((rel: (1.5, -2.5), to: struct-origin), "H", color: white, padding: 2pt, name: "H1")
atom((rel: (0, -3), to: struct-origin), "H", color: white, padding: 2pt, name: "H2")
atom((rel: (-1.5, -2.5), to: struct-origin), "H", color: white, padding: 2pt, name: "H3")
atom((rel: (-2, 0.75), to: struct-origin), "H", color: white, padding: 2pt, name: "H4")
atom((rel: (1, 2), to: struct-origin), "H", color: white, padding: 2pt, name: "H5")
// Add structure label - using fixed label-y
content(
(struct-x, label-y),
text(size: 14pt, weight: "bold")[Molecular Structure],
anchor: "center",
name: "struct-label-text",
)
// Calculate right edge of structure for arrow positioning
let struct-right-x = struct-x + 3.5
let struct-right = (struct-right-x, struct-y)
// Descriptor matrix - position relative to structure with closer spacing
let desc-x = struct-right-x + struct-desc-spacing
let desc-y = vertical-center + matrix-y-offset
let desc-origin = (desc-x, desc-y)
// Matrix data
let matrix-data = (
(74, 25, 39, 20, 3, 3, 3, 3, 3),
(25, 53, 31, 17, 7, 7, 2, 3, 2),
(39, 31, 37, 24, 3, 3, 3, 3, 3),
(20, 17, 24, 37, 2, 2, 6, 5, 5),
(3, 7, 3, 2, 0, 1, 0, 0, 0),
(3, 7, 3, 2, 1, 0, 0, 0, 0),
(3, 2, 3, 6, 0, 0, 0, 1, 1),
(3, 3, 3, 5, 0, 0, 1, 0, 1),
(3, 2, 3, 5, 0, 0, 1, 1, 0),
)
let cell-size = 0.6
let matrix-width = matrix-data.at(0).len() * cell-size
let matrix-height = matrix-data.len() * cell-size
// Draw matrix cells
for (row-idx, row) in matrix-data.enumerate() {
for (col-idx, value) in row.enumerate() {
let x = desc-x + col-idx * cell-size
let y = desc-y - row-idx * cell-size + 2.7 * cell-size
// Calculate color using the approach from heatmap.typ
let max-value = 74
rect(
(x, y),
(x + cell-size, y + cell-size),
fill: rgb(
90%, // Red stays constant at 90% for pastel effect
50% + value / max-value * 20%, // Green increases with value
50% - value / max-value * 20%, // Blue decreases with value
),
stroke: none,
name: "cell-" + str(row-idx) + "-" + str(col-idx),
)
content(
(x + cell-size / 2, y + cell-size / 2),
text(fill: if value < 40 { white } else { black }, size: 8pt)[#value],
anchor: "center",
name: "value-" + str(row-idx) + "-" + str(col-idx),
)
}
}
// Add descriptor label - using fixed label-y
content(
(desc-x + matrix-width / 2, label-y),
text(size: 14pt, weight: "bold")[Descriptor],
anchor: "center",
name: "desc-label-text",
)
// Calculate right edge of descriptor for arrow positioning
let desc-right-x = desc-x + matrix-width
let desc-right = (desc-right-x, desc-y)
// Neural network model - position relative to descriptor
let model-x = desc-right-x + component-spacing
let model-y = vertical-center
let model-origin = (model-x, model-y)
let layer-sep = 2.5
// Define neural network layers
let layers = (
// (x-pos, neuron-count, fill-color, label-prefix)
(model-x, 3, rgb("#40d0d0"), "i"), // Input layer - teal
(model-x + layer-sep, 4, rgb("#8080ff"), "h"), // Hidden layer - light blue
(model-x + 2 * layer-sep, 1, rgb("#f08040"), "o"), // Output layer - orange
)
// Draw all neurons FIRST (so connections appear behind nodes)
for (idx, (x, count, fill, prefix)) in layers.enumerate() {
for i in range(count) {
let y = vertical-center + (i - (count - 1) / 2) * 1.5
if idx == 2 {
y = vertical-center // Adjust output node position
}
neuron(
(x, y),
fill: fill,
text: $#prefix#(i+1)$,
name: prefix + "-" + str(i + 1),
)
}
}
// THEN draw connections using node names
for idx in range(layers.len() - 1) {
let (_, n1, _, prefix1) = layers.at(idx)
let (_, n2, _, prefix2) = layers.at(idx + 1)
// Connect every node in this layer to every node in the next layer
for i in range(n1) {
for j in range(n2) {
let node1-name = prefix1 + "-" + str(i + 1)
let node2-name = prefix2 + "-" + str(j + 1)
line(
(node1-name),
(node2-name),
stroke: rgb("#aaa") + 0.5pt,
)
}
}
}
// Add model label - using fixed label-y
content(
(model-x + layer-sep, label-y),
text(size: 14pt, weight: "bold")[Model],
anchor: "center",
name: "model-label-text",
)
// Calculate right edge of model for arrow positioning
let model-right-x = model-x + 2 * layer-sep + 1.5
let model-right = (model-right-x, model-y)
// Property - position relative to model with closer spacing
let property-x = model-right-x + model-prop-spacing
let property-y = vertical-center
let property-origin = (property-x, property-y)
// Draw property (alpha)
content(
property-origin,
text(size: 50pt, baseline: -3pt)[$alpha$],
anchor: "center",
name: "property",
)
// Add property label - using fixed label-y
content(
(property-x, label-y),
text(size: 14pt, weight: "bold")[Property],
anchor: "center",
name: "property-label-text",
)
// Define exact arrow length and positions for consistency
let arrow-length = 1.75
// Calculate midpoints between components for centered arrows
let desc-left-x = desc-x - 0.5
let model-left-x = model-x - 0.5
let property-left-x = property-x - 1.5
// Calculate midpoints for arrows
let midpoint1-x = (struct-right-x + desc-left-x) / 2
let midpoint2-x = (desc-right-x + model-left-x) / 2
let midpoint3-x = (model-right-x + property-left-x) / 2
// Draw arrows connecting the components
// First arrow: Molecular Structure to Descriptor
line(
(midpoint1-x - arrow-length / 2, vertical-center),
(midpoint1-x + arrow-length / 2, vertical-center),
..arrow-style,
name: "arrow1",
)
// Second arrow: Descriptor to Model
line(
(midpoint2-x - arrow-length / 2, vertical-center),
(midpoint2-x + arrow-length / 2, vertical-center),
..arrow-style,
name: "arrow2",
)
// Third arrow: Model to Property
line(
(midpoint3-x - arrow-length / 2, vertical-center),
(midpoint3-x + arrow-length / 2, vertical-center),
..arrow-style,
name: "arrow3",
)
})