Devlog #10

Since last time I’ve mostly been adding new physics, so here’s the list.

• Momentum space: The Radial view now shows how fast the electron is likely to be moving, not just where it is. This one is exact math too.
• Decay cascade: An excited hydrogen atom doesn’t fall straight to the bottom. It drops down step by step, and now you can watch every path it might take and how likely each one is.
• Lasers: There’s a new laser panel where you shine light on the atom and watch the electron flip back and forth between two levels (these are called Rabi oscillations).
• Relativity: For one-electron atoms you can now see the Dirac version of the wavefunction, which is what you get when you add Einstein’s relativity to quantum mechanics.
• The proton radius puzzle: The nucleus isn’t a perfect point. It has a size, and that shifts the energy levels a tiny bit. Two different experiments measured the proton’s size and got different answers, and you can see both predictions side by side.
• Antihydrogen: You can now make an atom out of antimatter. It matches normal hydrogen exactly, and the app explains why.
• Nuclear mass slider: You can drag the nucleus mass anywhere from as light as an electron to heavier than tritium and watch the atom change as you go.

All of this is getting pushed to the live site now, so it should be up soon!

Devlog #9

God Ive got a lot show since the last update.

First, the atom moves now. If you mix two states, you can watch the electron cloud slosh back and forth. Arrows show where the electron is flowing, and you can color the cloud by its phase.

I also changed the look to seem more natural and less AI, I added a plain white theme with a dark mode, grids on every graph, and buttons to save any graph as a picture or a spreadsheet.

Then I added a bunch of other features such as:

• Potassium and calcium, the first atoms past argon. There’s a mini experiment showing why 4s fills before 3d, even when 3d is lower in energy.
• A table that checks my calculations against real lab measurements for every atom from helium to calcium.
• sp, sp2 and sp3 hybrid orbitals, the shapes chemists use for bonds.
• Lines showing exactly where the electron can never be (nodes), and a scale bar in real units.
• A “measure the electron” button that drops dots one at a time until they build up the real shape.

Some smaller things:

• Every graph has a “Reproduce in Python” box with code you can copy.
• Any number can be cited with one click.
• You can export 3D models for printing.
• Shared links now preview the actual orbital.
• There’s an API guide, a changelog and a feedback link.

I also made the site faster by saving common results, and I fixed the phase colors so colorblind people can tell them apart.

I still need to test it in a browser and then deploy it so stay tuned for that!

Devlog #8

This update was mostly about cleaning things up.

Firstly, I went through the whole site with a checklist of things that make websites feel cheap or fake. I took out the gradients, made the rounded pill-shaped buttons and badges square, and replaced an emoji warning icon with a normal one. Then I added a Terms page and a Privacy page, linked at the bottom of the side panel. The privacy page explains what the app does and doesn’t track, which isn’t much. All of this was to remove any “ALL AI” msgs ive received

I also changed the license. AtomSim used to be MIT, which meant anyone could take it and sell it. Now it’s CC BY-NC 4.0, so people can still use it, share it and change it, as long as they credit me and don’t make money off it.

Every font on the site is now Poppins, and it’s bundled with the app so it doesn’t have to load from Google.

After that I reread all the text on the site and in the README and fixed anything that sounded robotic. That included a few curly quotes and one sentence that sounded like a press release. I also rewrote the line explaining “provenance” so it just says what it means.

All of that is live on the site now.

Next up is making the atom move. If you mix two states, the electron cloud sloshes back and forth at the exact frequency of the light the atom gives off. I’ve planned it out and I’m starting on it next. I also wrote down a big list of other ideas for later.

DEVLOG : 7?

Since that last update, the cleanup turned into actual features.

I finished the frontend narrator pass. Every disclosure string, every physics note, every view intro is now plain prose instead of the app talking about itself in first person.

Then I went after the parts of the app that were just annoying to use.

Plots are zoomable now. Wheel to zoom, drag to pan, on all five analytic views. I also built a small notation layer so the ASCII the engine emits gets typeset properly at render time, subscripts and superscripts where they belong, without dragging in a whole math library.

The big one was mobile. The app used to just refuse to render below a certain width. Now it works down to 320px: a proper mobile shell, view tabs instead of a sidebar list, controls that collapse, and per-view width floors so nothing spills sideways. That took a lot of small fixes I did not expect, a fixed SVG viewBox that hid fixed-width text, and an overflow rule that was already scrolling the page sideways before I touched anything.

After that, the URL got a real history. Back and Forward actually work now, and moving between orbitals pushes a history entry while flipping a display toggle just replaces one. Added a copy-link button and keyboard shortcuts for stepping through n, l, m and switching views.

Last thing, the title is now just AtomSim. The tagline was doing nothing for anyone.

Devlog #5 or 6???

Since the site went live, most of the work has been cleanup rather than new physics.

The whole app used to talk in first person. Every explanation said “I compute this” or “what I’m showing you.” It read like the code was narrating itself, which was odd. So I went through the entire Python engine module by module and rewrote it in plain technical prose. That’s done.

Then I started on the frontend, which had way more of it. The disclosure text, the physics notes under each equation, the view intros. That’s still in progress.

there were 2 things I had to be extra careful about. Some of those strings are checked word-for-word by tests, so rewording one has potential to break complete the build by itself.

In addition, I also tidied the repo layout for public viewing, fixed a deploy pipeline failure, and added privacy-safe visitor counting.

Right now i’m cutting padding, and pitching it so a high schooler can follow it without boring a physics grad.

Devlog: Phase 30 to now

Phase 30, Instrument frontend. Redesigned the UI to read like a physics instrument. Bundled the fonts, dropped four fields nothing actually measured, and learned that text-transform: uppercase turns 3d into 3D and α² into A², so uppercase is now confined to section headings only.

Phase 31, Guided tours. Added walkthroughs that drive the app for you. Nearly shipped a tour that quoted the wrong hydrogen energy because it skipped reduced mass, and fixed two spotlight rings that measured their target before layout settled.

Absorption band cleanup. Abutting sub-pixel SVG rects were drawing lines that weren’t in the data. Settled the mean vs deepest-per-column question and fixed decade ticks that failed at both ends of the axis.

Housekeeping. Moved specs and plans out to docs/specs and docs/plans. Personal ignores went into .git/info/exclude so no tracked file carries tooling names.

Rate limiting. Sized the burst from the app’s real fan-out per action rather than from click counts. The n=6 row plus an auto-refetch was quietly doubling the load.

Web hosting. Containerized and deployed to Fly.io as a single process. Cold start from a snapshot is about 1.6s, occasionally up to 22s if the snapshot gets discarded. Argon solves in 2.8s on the deployed box against 1.4s locally. Suspended machines cost nothing, so occasional use stays near a dollar or two a month.

Also added rate-limiter logging that identifies refused clients, and confirmed the proxy overwrites forged IP headers, so spoofing doesn’t get you past the limit.

DevLog #3: New Frontend, Plus Small Bits

Phase 22 to now.

P22, distinguishable electrons. Turned off exchange in Hartree-Fock. Electrons still repel, they just stop being identical. Marked COUNTERFACTUAL. Helium came back exactly zero, so it was gone.

P24, Pauli off. Dropped the occupancy cap and everything falls into the 1s. Argon becomes 1s^18 and the periodic table stops existing. P22’s slow convergence was shells, not exchange.

P25, isosurfaces. Never size a box on the grid you draw on. The fraction error bar is blind to the box. A 90% p orbital is one piece, not two lobes.

P26, HF in 3D. Now in Cloud, Plane, Radial and Surface. Whole-atom and one-orbital radii move opposite ways. Fidelity tiers were literals under the solve.

P27, total density. Added D(r), the shape both models describe. A uniform grid steps over the 1s peak, so the test asserts convergence rate, not tolerance.

P28, screened density. GSZ gets its own D(r). A density needs its own box. A log axis quietly breaks area = electron count.

P29, comparison. Both models on one axis, gap measured. Caught a noise floor, a real number printing as zero, and a wrong caption.

Sulfur, chlorine. Split ATOM_KEYS into identity and capability. Derive flags, never pass them. A client check exposed a deep-link race.

P30, instrument frontend. Fonts bundled for offline. –edge is a border colour, never a fill. Dropped four fields with no engine behind them. Uppercase turned 3d into 3D, so headings only now.

Plot polish. Zoomed line profile labels offsets from window centre, since absolute wavelengths printed the same string six times. Drew xyz axes through the cloud.

Absorption, curve of growth. Stopped a zero equivalent width stretching the axis 300 decades. The band drew anti-aliasing seams as absorption lines where transmission was really 0.98 to 1.00. It now bins one column per unit and draws the deepest sample, beside what a real detector pixel would see.

DevLog: Phase 18 to now

P18, line shapes. Real lines are not infinitely thin spikes. Atoms move (Doppler) and get jostled by neighbours (pressure), so each line spreads into a bell shape, a Voigt profile. I added that, plus a zoom so you can look at one line up close. The useful trick was a flux-closure check: whatever area a line has before broadening, it has to still have after. That caught two grid bugs that were invisible on screen.

P19, optical depth. Until now every line acted as if light escaped freely. In a thick gas strong lines saturate, so doubling the atoms stops doubling the brightness. That is the curve of growth. Lesson: decide which regime a line sits in from the physics, not by eyeballing the slope. Also the wavelength window has to widen as the column thickens, or you clip the wings you are trying to measure.

P20, absorption. The mirror of emission. Shine a continuum through the gas, look at what is missing. The trap was that 14 hydrogen lines land on only 6 distinct wavelengths, so matching a profile to its source line by wavelength quietly pairs the wrong ones. I key on the transition instead.

P21, Hartree-Fock. The big one. Instead of a fitted screening formula, each electron feels a potential built from all the others, solved over and over until it stops changing. That gets me sulfur and chlorine, which the old model could not touch, plus ions with no preset. Two things worth remembering: the solver’s own error bar was lying to me and needed re-deriving, and what made convergence fast was not a clever algorithm, it was the right mixing constant.

P22, cleanup. Made features honest about where they apply. The classical ghost and the force-law lab only make sense for one-electron atoms, so they explain themselves now instead of erroring on a screened atom. Fixed He+ breaking every API call, because the “+” was never URL-encoded. Unknown systems say so instead of spinning. Right now I am fixing hint text that escapes its panel on narrow screens.

Atom_Sim: Physics Simulator Dev Log

An atom simulator built on one rule: Every number has a label (exact, numerical, approximation, counterfactual, or visual_liberty). Unlabeled numbers are treated as bugs.

Stack: Python physics engine -> React + Three.js frontend.

Phase Logs

Phases 1–3: The Hydrogen Foundation

• Hydrogen Core: Uses exact math for energies and wavefunctions. Validates its electron clouds using statistical KS tests.
• Numerical Solver: Solves the Schrödinger equation for custom shapes. It calculates its own accuracy by halving the grid spacing.
• Constants Lab: Allows changing fundamental constants (hbar, e, c). It proves that changing individual units changes nothing if the ratio between them stays the same.
• Classical Ghost: Shows old Bohr orbits collapsing, proving why classical physics cannot explain atoms.

Phases 4–6: Altered Potential & Real Atoms

• Fake Physics: Simulates universes with non-standard forces (like Yukawa or power laws) under a clear warning banner.
• Screened Atoms: Models elements from Helium to Argon using historic 1974 data. If an element (like Sulfur or Chlorine) lacks clean data, it is left out entirely rather than guessed.

Phases 7–12: Fields, Relativity & Nuance

• Dirac Math: Tracks exact relativistic shifts and highlights what the math misses (the Lamb shift).
• External Fields: Simulates atoms splitting under magnetic fields (Zeeman effect) and electric fields (Stark effect).
• Hyperfine: Models the 21 cm hydrogen line using the precise electron-to-proton mass ratio.

Phases 13–17: Light, Speed & Thermodynamics

• Fast Math: Uses a custom integration trick to calculate atomic lifetimes exactly and 13x faster.
• Doublet Ratios: Proves via quantum math (Wigner 6j) why certain spectral lines are twice as bright as others.
• Heat Sliders: Combines Saha and Boltzmann equations to turn raw rates into actual visible light. Dragging the temperature slider smoothly hands Lyman lines over to Balmer lines.

Phase 18: Line Profiles (Current Work)

Replaces infinitely sharp lines with realistic Voigt profiles using three combined factors:

1. Natural Width: A Lorentzian shape caused by how fast an excited state decays.
2. Doppler Width: A Gaussian shape caused by thermal motion. Works perfectly for normal hydrogen, positronium, and muonic hydrogen.
3. Instrumental Width: A Gaussian blur based on the user’s chosen telescope or sensor resolution.

Note on Missing Physics: Collision/pressure broadening is not simulated. Instead of a text disclaimer, the app calculates how large that missing effect would be and prints the raw margin of error right next to the chart.

Core Development Rules

• No Smoke Tests: Every physics feature must pass an automated math test.
• No Live Fetches: All reference data is saved locally with a hard citation.
• No Silent Approximations: If the code cannot calculate something honestly, it stops and prints exactly what data is missing.