From d931bead0a849c6cd1d49777d7d000e9f7889e0a Mon Sep 17 00:00:00 2001 From: znetsixe Date: Mon, 11 May 2026 15:17:45 +0200 Subject: [PATCH] P9.3: wiki/Home.md following 14-section visual-first template + wiki:* scripts Auto-generated topic-contract + data-model sections via shared wikiGen script. Hand-written Mermaid diagrams for position-in-platform, code map, child registration, lifecycle, configuration, state chart (where applicable). Co-Authored-By: Claude Opus 4.7 (1M context) --- package.json | 9 +- wiki/Home.md | 285 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 291 insertions(+), 3 deletions(-) create mode 100644 wiki/Home.md diff --git a/package.json b/package.json index b67938f..50bec80 100644 --- a/package.json +++ b/package.json @@ -16,9 +16,12 @@ "license": "SEE LICENSE", "author": "P.R. van der Wilt", "main": "reactor.js", - "scripts": { - "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js" - }, + "scripts": { + "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js", + "wiki:contract": "node ../generalFunctions/scripts/wikiGen.js contract ./src/commands/index.js --write ./wiki/Home.md", + "wiki:datamodel": "node ../generalFunctions/scripts/wikiGen.js datamodel ./src/specificClass.js --write ./wiki/Home.md", + "wiki:all": "npm run wiki:contract && npm run wiki:datamodel" + }, "node-red": { "nodes": { "reactor": "reactor.js", diff --git a/wiki/Home.md b/wiki/Home.md new file mode 100644 index 0000000..4f2177f --- /dev/null +++ b/wiki/Home.md @@ -0,0 +1,285 @@ +# reactor + +> **Reflects code as of `b8247fc` · regenerated `2026-05-11` via `npm run wiki:all`** +> If this banner is stale, the page may be out of date. Treat as informative, not authoritative. + +## 1. What this node is + +**reactor** is an S88 Unit that wraps an ASM3 biological-process engine — either a CSTR (fully mixed tank) or a PFR (plug-flow with axial dispersion). It integrates 13 species (S_O, S_NH, X_H, X_TS, …) and emits the effluent vector each tick. Drives a settler downstream and accepts a recirculation pump child. + +## 2. Position in the platform + +```mermaid +flowchart LR + upstream[reactor
upstream
Unit]:::unit + reactor[reactor
Unit]:::unit + settler[settler
downstream
Unit]:::unit + pump[rotatingMachine
downstream
Equipment]:::equip + tsens[measurement
temperature
atequipment]:::ctrl + osens[measurement
oxygen
position]:::ctrl + + upstream -.stateChange.-> reactor + reactor -->|Fluent inlet=0| settler + pump -->|child.register downstream| reactor + tsens -->|temperature.measured.atequipment| reactor + osens -->|quantity (oxygen).measured.<position>| reactor + classDef unit fill:#50a8d9,color:#000 + classDef equip fill:#86bbdd,color:#000 + classDef ctrl fill:#a9daee,color:#000 +``` + +S88 colours: Unit `#50a8d9`, Equipment `#86bbdd`, Control Module `#a9daee`. Source of truth: `.claude/rules/node-red-flow-layout.md`. + +## 3. Capability matrix + +| Capability | Status | Notes | +|---|---|---| +| ASM3 13-species ODE integration | ✅ | CSTR + PFR engines under `kinetics/`. | +| CSTR (fully mixed) | ✅ | Single concentration vector per tick. | +| PFR (axial discretization) | ✅ | `resolution_L` grid cells; emits `GridProfile` alongside `Fluent`. | +| Multi-inlet mixing | ✅ | `n_inlets`; each inlet receives its own `data.fluent` with `inlet` index. | +| Temperature reconcile from measurement | ✅ | `temperature.measured.atEquipment` writes `engine.temperature`. | +| Oxygen reconcile (PFR) | ✅ | `quantity (oxygen).measured.` maps to nearest grid cell. | +| KLa-driven aeration | ✅ | `reactor.kla` > 0 enables internal mass transfer; falls back to `data.otr`. | +| Speed-up factor (sim time) | ✅ | `reactor.speedUpFactor` accelerates wall-clock → process time. | +| Dispersion override (PFR) | ✅ | `data.dispersion` updates axial `D`. | +| Hot-swap engine type | ❌ | `reactor_type` is read once in `configure()`. | + +## 4. Code map + +```mermaid +flowchart TB + subgraph nodeRED["nodeClass.js — adapter (BaseNodeAdapter)"] + nc["buildDomainConfig()
static DomainClass = Reactor
static commands"] + end + subgraph domain["specificClass.js — orchestrator (BaseDomain)"] + sc["Reactor.configure()
flatten config → build engine
ChildRouter rules"] + end + subgraph kinetics["src/kinetics/"] + be["baseEngine.js
shared ASM3 rate vector"] + cstr["cstr.js
0-D integrator"] + pfr["pfr.js
spatial discretization + dispersion"] + end + subgraph commands["src/commands/"] + cmds["index.js + handlers.js
6 input topics"] + end + sc --> be + sc --> cstr + sc --> pfr + nc --> sc + nc --> cmds +``` + +| Module | Owns | Read first if you're changing… | +|---|---|---| +| `kinetics/baseEngine.js` | ASM3 stoichiometry + rate vector + species list. | Stoichiometric matrix, kinetic constants. | +| `kinetics/cstr.js` | 0-D CSTR integrator + `_connectMeasurement` + `_connectReactor`. | Mixed-tank behaviour, child wiring. | +| `kinetics/pfr.js` | Axial discretization, dispersion, grid profile emission. | PFR-specific behaviour, grid math. | +| `commands/` | 6 input descriptors + handlers (clock, fluent, OTR, temperature, dispersion, child). | Inbound topic API, alias deprecation. | +| `reaction_modules/` | Optional plug-in reaction modules (legacy — not yet refactored). | Adding new bio-process modules. | +| `additional_nodes/` | Sibling Node-RED nodes (`recirculation-pump`, `settling-basin`) shipped from this repo. | Cross-node deploy in same package. | + +## 5. Topic contract + +> **Auto-generated** from `src/commands/index.js`. Do NOT hand-edit between the markers. Re-run `npm run wiki:contract`. + + + +| Canonical topic | Aliases | Payload | Effect | +|---|---|---|---| +| `data.clock` | `clock` | `any` | Pushes a value into the node's measurement stream. | +| `data.fluent` | `Fluent` | `object` | Pushes a value into the node's measurement stream. | +| `data.otr` | `OTR` | `any` | Pushes a value into the node's measurement stream. | +| `data.temperature` | `Temperature` | `any` | Pushes a value into the node's measurement stream. | +| `data.dispersion` | `Dispersion` | `any` | Pushes a value into the node's measurement stream. | +| `child.register` | `registerChild` | `any` | Parent/child plumbing — registers or unregisters a child node. | + + + +## 6. Child registration + +```mermaid +flowchart LR + subgraph kids["accepted children (softwareType)"] + m_t["measurement
temperature"]:::ctrl + m_o["measurement
quantity (oxygen)"]:::ctrl + r_up["reactor
upstream"]:::unit + end + m_t -->|temperature.measured.atEquipment| h_meas[engine._connectMeasurement] + m_o -->|quantity (oxygen).measured.<pos>| h_meas + r_up -.stateChange.-> h_react[engine._connectReactor] + h_meas --> reconcile[reconcile T / O2 into engine state] + h_react --> pull[pull upstream effluent → Fs/Cs_in] + classDef ctrl fill:#a9daee,color:#000 + classDef unit fill:#50a8d9,color:#000 +``` + +| softwareType | filter | wired to | side-effect | +|---|---|---|---| +| `measurement` | any | `engine._connectMeasurement` | `temperature.measured.atEquipment` → `engine.temperature`. PFR additionally honours `quantity (oxygen).measured.` → nearest grid cell DO. | +| `reactor` | upstream | `engine._connectReactor` | Subscribes to upstream reactor's `stateChange`; pulls effluent into `Fs[0]` / `Cs_in[0]` before next integration step. | + +## 7. Lifecycle — what one `data.clock` advance does + +```mermaid +sequenceDiagram + participant clock as clock injector + participant reactor as reactor + participant engine as kinetics engine + participant downstream as settler / next reactor + participant out as Port-0 output + + clock->>reactor: data.clock { timestamp } + reactor->>engine: updateState(timestamp) + Note over engine: n_iter steps,
each timeStep × speedUpFactor + engine->>engine: integrate ASM3 rates + engine->>engine: emit 'stateChange' + reactor->>reactor: notifyOutputChanged + reactor->>out: Fluent { inlet=0, F, C[13] } + alt PFR + reactor->>out: GridProfile { grid, n_x, d_x, … } + end + out->>downstream: Fluent envelope +``` + +`stateChange` re-emits on `reactor.emitter` (BaseDomain emitter) so downstream reactors / settlers can listen. The effluent emission goes through the BaseNodeAdapter tick pipeline. + +## 8. Data model — `getOutput()` + +Port-0 process payload is the `Fluent` envelope (+ optional `GridProfile` for PFR). Port-1 telemetry is the scalar snapshot below. + + + +| Key | Type | Unit | Sample | +|---|---|---|---| +| `S_HCO` | number | — | `5` | +| `S_I` | number | — | `30` | +| `S_N2` | number | — | `0` | +| `S_NH` | number | — | `25` | +| `S_NO` | number | — | `0` | +| `S_O` | number | — | `0` | +| `S_S` | number | — | `70` | +| `X_A` | number | — | `200` | +| `X_H` | number | — | `2000` | +| `X_I` | number | — | `1000` | +| `X_S` | number | — | `100` | +| `X_STO` | number | — | `0` | +| `X_TS` | number | — | `3500` | +| `flow_total` | number | — | `0` | +| `temperature` | number | — | `20` | + + + +**Concrete sample** (CSTR mid-integration, nitrifying): + +```json +{ + "flow_total": 1000, + "temperature": 15.2, + "S_O": 2.1, + "S_I": 30, + "S_S": 12.4, + "S_NH": 0.8, + "S_N2": 4.3, + "S_NO": 18.6, + "S_HCO": 4.2, + "X_I": 1050, + "X_S": 65, + "X_H": 2150, + "X_STO": 4.5, + "X_A": 215, + "X_TS": 3680 +} +``` + +Species ordering follows ASM3: indices 0–6 are soluble, 7–12 are particulate. `flow_total` is the effluent flow (m³/d); the reactor uses days as the time unit internally. + +## 9. Configuration — editor form ↔ config keys + +```mermaid +flowchart TB + subgraph editor["Node-RED editor form"] + f1[Reactor type CSTR / PFR] + f2[Volume m3] + f3[Length m + resolution] + f4[Alpha dispersion] + f5[KLa 1/h] + f6[Time step + speed-up] + f7[Initial state 13 species] + end + subgraph config["Domain config slice"] + c1[reactor.reactor_type] + c2[reactor.volume] + c3[reactor.length
reactor.resolution_L] + c4[reactor.alpha] + c5[reactor.kla] + c6[reactor.timeStep
reactor.speedUpFactor] + c7[initialState.* ASM3 keys] + end + f1 --> c1 + f2 --> c2 + f3 --> c3 + f4 --> c4 + f5 --> c5 + f6 --> c6 + f7 --> c7 +``` + +| Form field | Config key | Default | Range | Where used | +|---|---|---|---|---| +| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` | engine selection in `_buildEngine` | +| Volume (m³) | `reactor.volume` | `1000` | > 0 | residence time, mass balance | +| Length (m) | `reactor.length` | `10` | > 0 | PFR only — axial extent | +| Resolution L | `reactor.resolution_L` | `10` | ≥ 1 | PFR grid cell count | +| Alpha | `reactor.alpha` | `0.5` | 0–1 | dispersion vs plug-flow blend | +| Inlets | `reactor.n_inlets` | `1` | ≥ 1 | `Fs[]` / `Cs_in[]` array sizes | +| KLa (1/h) | `reactor.kla` | `0` | ≥ 0 | aeration mass transfer (NaN → use `data.otr`) | +| Time step (h) | `reactor.timeStep` | `0.001` | ≥ 0.0001 | integrator inner step | +| Speed-up factor | `reactor.speedUpFactor` | `1` | ≥ 1 | wall-clock → process-time multiplier | +| Initial S_NH | `initialState.S_NH` | `25` | ≥ 0 (mg/L) | starting ammonium | +| Initial X_H | `initialState.X_H` | `2000` | ≥ 0 (mg/L) | starting heterotroph biomass | +| Initial X_A | `initialState.X_A` | `200` | ≥ 0 (mg/L) | starting autotroph biomass — must be ≥ ~50 for nitrification | +| Initial X_TS | `initialState.X_TS` | `3500` | ≥ 0 (mg/L) | starting TSS — drives settler split | + +## 10. State chart + +Skipped — reactor has no FSM. It runs continuous-state ODE integration; the engine's only stateful event is `stateChange`, fired after every successful integration advance. See section 7 for the integration sequence. + +## 11. Examples + +| Tier | File | What it shows | Status | +|---|---|---|---| +| Basic | `examples/basic.flow.json` | CSTR with one inlet, watch `Fluent` effluent | ✅ in repo | +| Integration | `examples/integration.flow.json` | upstream reactor → reactor → settler chain | ✅ in repo | +| Edge | `examples/edge.flow.json` | PFR with dispersion + multi-inlet | ✅ in repo | +| Companions | `additional_nodes/*` | recirculation-pump + settling-basin Node-RED nodes shipped from this repo | ✅ in repo | + +One screenshot per tier where helpful. PNG ≤ 200 KB under `wiki/_partial-screenshots/reactor/`. + +## 12. Debug recipes + +| Symptom | First thing to check | Where to look | +|---|---|---| +| Nitrification doesn't proceed (S_NH stays high) | `initialState.X_A` must be ≥ ~50 mg/L. Defaulting to `0.001` (a known footgun) means no autotrophs. | `generalFunctions/src/configs/reactor.json` | +| `Fluent` effluent flow zero | No `data.clock` ticks arriving, or `data.fluent` never set `Fs[0] > 0`. | `commands/handlers.js`, engine `setInfluent` | +| PFR `GridProfile` not emitted | `reactor_type` set to `CSTR` — only PFR emits grid. | `_buildEngine` switch | +| Settler downstream not updating | `stateChange` event listener path: settler must subscribe to `reactor.emitter`, NOT `reactor.measurements.emitter`. | settler `_connectReactor` | +| Temperature reconcile silently ignored | Child measurement's `asset.type` not `temperature` exactly, or `positionVsParent` not `atEquipment`. | `engine._connectMeasurement` | +| Integrator slow / stalls | `reactor.timeStep` too small for `speedUpFactor`. Internal `n_iter` count blows up. | `engine.updateState` | +| `wiki:datamodel` script slow / hangs | `mathjs` cold-start ~13 s; instantiation depends on it transitively. See known-limitations row 1. | `kinetics/baseEngine.js` | + +## 13. When you would NOT use this node + +- Use reactor for **ASM3 biological treatment** modelling (activated sludge, nitrification, denitrification). For aerobic-only or simpler kinetics, the ASM3 species vector is overkill. +- Don't use reactor for a passive equalisation tank — the kinetics engines assume reactions are happening. +- Skip reactor when you only need a residence-time delay; a simple buffer node is lighter and doesn't require `mathjs`. + +## 14. Known limitations / current issues + +| # | Issue | Tracked in | +|---|---|---| +| 1 | `mathjs` cold-start adds ~13 s to first `require()` — `wiki:datamodel` auto-gen may time out on the 60 s wrapper. Falls back to the hand-curated `concrete sample` block. | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" | +| 2 | `initialState.X_A` default of `200` mg/L is correct; older config snapshots used `0.001` which silently disabled nitrification. Verify on every new deploy. | `generalFunctions/src/configs/reactor.json` | +| 3 | `getEffluent` shape historically varied (array vs single envelope) — settler's `_connectReactor` tolerates both. Don't break the contract without updating settler. | `nodes/settler/src/specificClass.js → _connectReactor` | +| 4 | `additional_nodes/recirculation-pump` and `settling-basin` are legacy companions — not yet refactored to BaseDomain. | P6.5 follow-up | +| 5 | `reaction_modules/` is a legacy plug-in directory not consumed by the current engines. Removal pending. | P6.5 follow-up |