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UPDATE_SITE.md

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Updating the ParticleGraph Documentation Site

Prerequisites

Before updating site content, ensure the exploration has produced new data:

  • Montages, videos, and UCB trees in the media directory (see below)
  • Updated diffusiophoresis_Claude_analysis.md and diffusiophoresis_Claude_memory.md

Quick Render

cd /workspace/ParticleGraph
quarto render

Output goes to _site/.

Clean Rebuild (stale images)

If the site still shows old montages (e.g. bottom-right panel printing metrics text instead of the flow field), delete both _site/ and the Quarto cache:

rm -rf _site .quarto
quarto render

Image / Video Source

All media must come from one directory only:

log/Claude_exploration/instruction_diffusiophoresis_parallel/
  montage/   montage_iter_NNN.png   (iters 003-088)
  figure/    figure_iter_NNN.png
  video/     video_iter_NNN.mp4
  tree/      ucb_tree_iter_NNN.png  (every 8 iters)
  config/    iter_NNN_slot_NN.yaml

The old path graphs_data/diffusiophoresis/diffusiophoresis_Claude/ is deprecated and must not be used — those images have a metrics text panel instead of the flow field in the bottom-right.

Montage layout (4 rows x 10 time-steps)

Row Content
1 Chemical field C1
2 Particles with velocity arrows
3 C1/C2 fields with particle overlays
4 Particle flow field (replaced old metrics panel)

Quarto Source Files

File Content Last Update
_quarto.yml Site config, navbar, theme
index.qmd Landing page Block 11
field-field.qmd Field-Field (Turing patterns) Block 11
field-particle.qmd Diffusiophoresis
particle-field.qmd Particle-Field
particle-particle.qmd Particle-Particle
brusselator.qmd Brusselator model (hex + stripe + NLD labyrinthine/vermiform) Block 11
grayscott.qmd Gray-Scott model
fhn.qmd FitzHugh-Nagumo model
schnakenberg.qmd Schnakenberg model
llm-exploration.qmd Exploration gallery (montages, videos, UCB trees) Block 11
mechanochemical.qmd Mechanochemical / MPM extension

Update Procedure

Step 1: Update Quarto Content

Update these .qmd files based on new discoveries in diffusiophoresis_Claude_memory.md:

  1. llm-exploration.qmd — Add new block gallery, update regime comparison, principles, score table, UCB trees
  2. brusselator.qmd — Add new pattern modes if discovered (e.g. NLD labyrinthine/vermiform from Block 11)
  3. index.qmd — Update date, iteration count, discovery summary
  4. field-field.qmd — Update model descriptions if new capabilities discovered
  5. Other model pages as needed

Step 2: Render the Site

cd /workspace/ParticleGraph
rm -rf _site .quarto
quarto render

Step 3: Push to GitHub

cd /workspace/ParticleGraph
git add -A
git commit -m "Update site with Block N results"
git push

Adding New Iterations

Add to llm-exploration.qmd:

![Caption](log/Claude_exploration/instruction_diffusiophoresis_parallel/montage/montage_iter_NNN.png){.lightbox group="blockN"}

{{< video log/Claude_exploration/instruction_diffusiophoresis_parallel/video/video_iter_NNN.mp4 >}}

NFS Mount

/workspace is mounted from prfs.hhmi.org:/groups/saalfeld/home/allierc/Graph, so both paths point to the same files.

Current State (Block 11, 88 iterations)

  • Best scores: 8/10 (Iters 14, 45, 53 — 3-type Brusselator flower/mandala)
  • Novel patterns: Labyrinthine Turing (Iter 83), vermiform filaments (Iter 87)
  • 20 established principles across 11 blocks
  • 5 PDE models tested, only Brusselator produces non-radial morphologies
  • NLD code modification (Block 11): nonlinear diffusion enables labyrinthine/vermiform modes