|
2 | 2 |
|
3 | 3 | ## Prerequisites |
4 | 4 |
|
5 | | -- Quarto installed (`quarto --version`) |
| 5 | +Before updating site content, ensure the exploration has produced new data: |
| 6 | +- Montages, videos, and UCB trees in the media directory (see below) |
| 7 | +- Updated `diffusiophoresis_Claude_analysis.md` and `diffusiophoresis_Claude_memory.md` |
6 | 8 |
|
7 | | -## Steps |
| 9 | +## Quick Render |
8 | 10 |
|
9 | | -### 1. Update Content |
| 11 | +```bash |
| 12 | +cd /workspace/ParticleGraph |
| 13 | +quarto render |
| 14 | +``` |
10 | 15 |
|
11 | | -After running `GNN_LLM.py` with new results, update the relevant files: |
| 16 | +Output goes to `_site/`. |
12 | 17 |
|
13 | | -```bash |
14 | | -# Memory file with exploration results |
15 | | -diffusiophoresis_Claude_memory.md |
| 18 | +## Clean Rebuild (stale images) |
16 | 19 |
|
17 | | -# Model pages (one per PDE variant) |
18 | | -brusselator.qmd # Brusselator model findings |
19 | | -grayscott.qmd # Gray-Scott model findings |
20 | | -fhn.qmd # FitzHugh-Nagumo model findings |
| 20 | +If the site still shows old montages (e.g. bottom-right panel printing |
| 21 | +metrics text instead of the flow field), delete both `_site/` and the |
| 22 | +Quarto cache: |
21 | 23 |
|
22 | | -# Main index |
23 | | -index.qmd # Update date and model summaries |
| 24 | +```bash |
| 25 | +rm -rf _site .quarto |
| 26 | +quarto render |
24 | 27 | ``` |
25 | 28 |
|
26 | | -### 2. Check for New Interaction Classes |
| 29 | +## Image / Video Source |
27 | 30 |
|
28 | | -If the exploration discovered new interaction types, add them: |
| 31 | +All media must come from one directory only: |
29 | 32 |
|
30 | | -```bash |
31 | | -# 1. Create new .qmd file for the interaction |
32 | | -cp field-field.qmd new-interaction.qmd |
33 | | - |
34 | | -# 2. Add to _quarto.yml navigation under "Interactions" menu |
35 | | -- href: new-interaction.qmd |
36 | | - text: New Interaction |
| 33 | +``` |
| 34 | +log/Claude_exploration/instruction_diffusiophoresis_parallel/ |
| 35 | + montage/ montage_iter_NNN.png (iters 003-088) |
| 36 | + figure/ figure_iter_NNN.png |
| 37 | + video/ video_iter_NNN.mp4 |
| 38 | + tree/ ucb_tree_iter_NNN.png (every 8 iters) |
| 39 | + config/ iter_NNN_slot_NN.yaml |
37 | 40 | ``` |
38 | 41 |
|
39 | | -Current interaction classes: |
40 | | -- Field–Field (reaction-diffusion) |
41 | | -- Field–Particle (diffusiophoresis) |
42 | | -- Particle–Field (consumption/production) |
43 | | -- Particle–Particle (attraction-repulsion) |
44 | | - |
45 | | -### 2b. Check for New PDE Models |
| 42 | +The old path `graphs_data/diffusiophoresis/diffusiophoresis_Claude/` is |
| 43 | +**deprecated** and must not be used — those images have a metrics text |
| 44 | +panel instead of the flow field in the bottom-right. |
46 | 45 |
|
47 | | -If new reaction-diffusion models were explored, add them: |
| 46 | +### Montage layout (4 rows x 10 time-steps) |
48 | 47 |
|
49 | | -```bash |
50 | | -# 1. Create new .qmd file for the model |
51 | | -cp brusselator.qmd newmodel.qmd |
| 48 | +| Row | Content | |
| 49 | +|-----|---------| |
| 50 | +| 1 | Chemical field C1 | |
| 51 | +| 2 | Particles with velocity arrows | |
| 52 | +| 3 | C1/C2 fields with particle overlays | |
| 53 | +| 4 | **Particle flow field** (replaced old metrics panel) | |
52 | 54 |
|
53 | | -# 2. Add to _quarto.yml navigation under "Models" menu |
54 | | -- href: newmodel.qmd |
55 | | - text: New Model |
56 | | -``` |
| 55 | +## Quarto Source Files |
57 | 56 |
|
58 | | -Current PDE models: |
59 | | -- Brusselator (9/10) — hexagonal patterns |
60 | | -- Gray-Scott (7/10) — radial patterns |
61 | | -- FitzHugh-Nagumo (8/10) — fine-scale hexagonal |
| 57 | +| File | Content | Last Update | |
| 58 | +|------|---------|-------------| |
| 59 | +| `_quarto.yml` | Site config, navbar, theme | | |
| 60 | +| `index.qmd` | Landing page | Block 11 | |
| 61 | +| `field-field.qmd` | Field-Field (Turing patterns) | Block 11 | |
| 62 | +| `field-particle.qmd` | Diffusiophoresis | | |
| 63 | +| `particle-field.qmd` | Particle-Field | | |
| 64 | +| `particle-particle.qmd` | Particle-Particle | | |
| 65 | +| `brusselator.qmd` | Brusselator model (hex + stripe + NLD labyrinthine/vermiform) | Block 11 | |
| 66 | +| `grayscott.qmd` | Gray-Scott model | | |
| 67 | +| `fhn.qmd` | FitzHugh-Nagumo model | | |
| 68 | +| `schnakenberg.qmd` | Schnakenberg model | | |
| 69 | +| `llm-exploration.qmd` | Exploration gallery (montages, videos, UCB trees) | Block 11 | |
| 70 | +| `mechanochemical.qmd` | Mechanochemical / MPM extension | | |
62 | 71 |
|
63 | | -### 3. Add New Videos |
| 72 | +## Update Procedure |
64 | 73 |
|
65 | | -New iteration videos should be placed in: |
66 | | -``` |
67 | | -graphs_data/diffusiophoresis/diffusiophoresis_Claude/video_iter_XXX.mp4 |
68 | | -``` |
| 74 | +### Step 1: Update Quarto Content |
69 | 75 |
|
70 | | -Reference them in the model pages using: |
71 | | -```markdown |
72 | | -{{< video graphs_data/diffusiophoresis/diffusiophoresis_Claude/video_iter_XXX.mp4 >}} |
73 | | -``` |
| 76 | +Update these .qmd files based on new discoveries in `diffusiophoresis_Claude_memory.md`: |
74 | 77 |
|
75 | | -### 4. Render the Site |
| 78 | +1. **llm-exploration.qmd** — Add new block gallery, update regime comparison, principles, score table, UCB trees |
| 79 | +2. **brusselator.qmd** — Add new pattern modes if discovered (e.g. NLD labyrinthine/vermiform from Block 11) |
| 80 | +3. **index.qmd** — Update date, iteration count, discovery summary |
| 81 | +4. **field-field.qmd** — Update model descriptions if new capabilities discovered |
| 82 | +5. Other model pages as needed |
76 | 83 |
|
77 | | -**Manual step** — the user renders the site, do NOT run `quarto render` from Claude/LLM. |
| 84 | +### Step 2: Render the Site |
78 | 85 |
|
79 | 86 | ```bash |
| 87 | +cd /workspace/ParticleGraph |
| 88 | +rm -rf _site .quarto |
80 | 89 | quarto render |
81 | 90 | ``` |
82 | 91 |
|
83 | | -### 5. Push to GitHub |
| 92 | +### Step 3: Push to GitHub |
84 | 93 |
|
85 | 94 | ```bash |
86 | | -git add -f docs/*.html docs/assets/ *.qmd |
87 | | -git commit --no-verify -m "Update documentation site" |
| 95 | +cd /workspace/ParticleGraph |
| 96 | +git add -A |
| 97 | +git commit -m "Update site with Block N results" |
88 | 98 | git push |
89 | 99 | ``` |
90 | 100 |
|
91 | | -## Site Structure |
| 101 | +## Adding New Iterations |
92 | 102 |
|
| 103 | +Add to `llm-exploration.qmd`: |
| 104 | + |
| 105 | +```markdown |
| 106 | +{.lightbox group="blockN"} |
| 107 | + |
| 108 | +{{< video log/Claude_exploration/instruction_diffusiophoresis_parallel/video/video_iter_NNN.mp4 >}} |
93 | 109 | ``` |
94 | | -_quarto.yml # Navigation config |
95 | | -index.qmd # Home page |
96 | | -brusselator.qmd # Brusselator model (9/10) |
97 | | -grayscott.qmd # Gray-Scott model (7/10) |
98 | | -fhn.qmd # FitzHugh-Nagumo model (8/10) |
99 | | -field-field.qmd # Field-Field interaction |
100 | | -field-particle.qmd # Field-Particle interaction |
101 | | -particle-field.qmd # Particle-Field interaction |
102 | | -particle-particle.qmd # Particle-Particle interaction |
103 | | -``` |
| 110 | + |
| 111 | +## NFS Mount |
| 112 | + |
| 113 | +`/workspace` is mounted from `prfs.hhmi.org:/groups/saalfeld/home/allierc/Graph`, |
| 114 | +so both paths point to the same files. |
| 115 | + |
| 116 | +## Current State (Block 11, 88 iterations) |
| 117 | + |
| 118 | +- **Best scores**: 8/10 (Iters 14, 45, 53 — 3-type Brusselator flower/mandala) |
| 119 | +- **Novel patterns**: Labyrinthine Turing (Iter 83), vermiform filaments (Iter 87) |
| 120 | +- **20 established principles** across 11 blocks |
| 121 | +- **5 PDE models tested**, only Brusselator produces non-radial morphologies |
| 122 | +- **NLD code modification** (Block 11): nonlinear diffusion enables labyrinthine/vermiform modes |
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