From d735f9485ce732d128ad8a1b305266d6b38ced74 Mon Sep 17 00:00:00 2001 From: znetsixe Date: Mon, 11 May 2026 21:07:07 +0200 Subject: [PATCH] docs(wiki): rewrite Home.md to full 14-section visual-first template MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Banner updated to c84dd78 / 2026-05-11 - Section 2: add diffuser (data.otr path, not child-register), upstream reactor stateChange, settler downstream; switch to ~~~mermaid fences - Section 4: accurate code-map — cstr/pfr extend baseEngine, not peer nodes - Section 6: split measurement into temperature + oxygen(PFR) rows; clarify diffuser is NOT a registered child; switch to ~~~mermaid fences - Section 7: expand sequence with n_iter formula, DO capping, GridProfile alt - Section 9: correct timeStep unit note (schema h vs HTML label s), add all 13 init fields, note X_A HTML default footgun, enum-casing note in cell - Section 14: add row #6 (reactor_type enum lowercasing / toUpperCase guard) and row #7 (timeStep unit mismatch — label vs schema vs engine conversion) AUTOGEN markers (topic-contract, data-model) untouched — regenerated clean. Co-Authored-By: Claude Sonnet 4.6 --- wiki/Home.md | 153 ++++++++++++++++++++++++++++----------------------- 1 file changed, 84 insertions(+), 69 deletions(-) diff --git a/wiki/Home.md b/wiki/Home.md index 7260401..6ee36fb 100644 --- a/wiki/Home.md +++ b/wiki/Home.md @@ -1,6 +1,6 @@ # reactor -> **Reflects code as of `b8247fc` · regenerated `2026-05-11` via `npm run wiki:all`** +> **Reflects code as of `c84dd78` · 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 If this banner is stale, the page may be out of date.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 @@ -9,27 +9,32 @@ ## 2. Position in the platform -```mermaid +~~~mermaid flowchart LR upstream[reactor
upstream
Unit]:::unit reactor[reactor
Unit]:::unit settler[settler
downstream
Unit]:::unit - pump[rotatingMachine
downstream
Equipment]:::equip + diffuser[diffuser
Equipment]:::equip tsens[measurement
temperature
atequipment]:::ctrl - osens[measurement
oxygen
position]:::ctrl + osens[measurement
oxygen
at distance]:::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 + settler -.stateChange.-> reactor + diffuser -->|data.otr| reactor + tsens -->|child.register| reactor + osens -->|child.register| reactor + tsens -->|temperature.measured.atEquipment| reactor + osens -->|quantity(oxygen).measured.distance| 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`. +reactor sits at the Unit level. A diffuser (Equipment) sends aeration rates via `data.otr` — it is NOT registered as a child. Measurement children (Control Module) register and supply temperature or dissolved-oxygen reconciliation. Settler is a downstream Unit that listens to `stateChange` to pull effluent; an upstream reactor drives this reactor the same way. + ## 3. Capability matrix | Capability | Status | Notes | @@ -38,7 +43,7 @@ S88 colours: Unit `#50a8d9`, Equipment `#86bbdd`, Control Module `#a9daee`. Sour | 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`. | +| Temperature reconcile from measurement | ✅ | `temperature.measured.atEquipment` writes `engine.temperature`. Code constant: `POSITIONS.AT_EQUIPMENT`. | | 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. | @@ -47,28 +52,28 @@ S88 colours: Unit `#50a8d9`, Equipment `#86bbdd`, Control Module `#a9daee`. Sour ## 4. Code map -```mermaid +~~~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"] + sc["Reactor.configure()
_flattenEngineConfig()
_buildEngine() → CSTR or PFR
ChildRouter.onRegister 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"] + be["baseEngine.js
BaseReactorEngine
influent state, OTR, T
_connectMeasurement / _connectReactor
updateState() → n_iter ticks"] + cstr["cstr.js
Reactor_CSTR extends BaseReactorEngine
Forward-Euler 0-D integrator"] + pfr["pfr.js
Reactor_PFR extends BaseReactorEngine
FD spatial grid + Danckwerts BC"] end subgraph commands["src/commands/"] - cmds["index.js + handlers.js
6 input topics"] + cmds["index.js — 6 descriptors
handlers.js — 6 pure fns"] end - sc --> be - sc --> cstr - sc --> pfr nc --> sc nc --> cmds -``` + sc --> be + cstr --> be + pfr --> be +~~~ | Module | Owns | Read first if you're changing… | |---|---|---| @@ -98,51 +103,55 @@ flowchart TB ## 6. Child registration -```mermaid +~~~mermaid flowchart LR subgraph kids["accepted children (softwareType)"] - m_t["measurement
temperature"]:::ctrl - m_o["measurement
quantity (oxygen)"]:::ctrl - r_up["reactor
upstream"]:::unit + m_t["measurement
temperature
positionVsParent=atEquipment"]:::ctrl + m_o["measurement
quantity (oxygen)
positionVsParent=distance (numeric)"]:::ctrl + r_up["reactor
positionVsParent=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] + m_t -->|temperature.measured.atEquipment| h_meas["engine._connectMeasurement
(baseEngine.js)"] + m_o -->|quantity(oxygen).measured.distance| h_meas + r_up -.stateChange.-> h_react["engine._connectReactor
(baseEngine.js)"] + h_meas --> reconcile["reconcile T → engine.temperature
reconcile O2 → state grid cell (PFR only)"] + h_react --> pull["pull upstream getEffluent
→ Fs[0] / Cs_in[0] before next tick"] 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. | +| `measurement` | `asset.type = temperature`, `positionVsParent = atEquipment` | `engine._connectMeasurement` | Writes `engine.temperature`. CSTR only honours temperature; PFR additionally reconciles `quantity (oxygen).measured.` (numeric position) → nearest grid cell DO. | +| `measurement` | `asset.type = quantity (oxygen)`, `positionVsParent = ` | `engine._connectMeasurement` → `pfr._updateMeasurement` | PFR only: maps measurement to nearest grid cell by `round(pos / length × n_x)`. | +| `reactor` | `positionVsParent = upstream` | `engine._connectReactor` | Subscribes to upstream reactor's `stateChange`; pulls `getEffluent` into `Fs[0]` / `Cs_in[0]` before next integration step. | + +`diffuser` is NOT a registered child — it feeds aeration via `data.otr` on Port 0. No child-registration handshake is involved. ## 7. Lifecycle — what one `data.clock` advance does -```mermaid +~~~mermaid sequenceDiagram participant clock as clock injector - participant reactor as reactor - participant engine as kinetics engine + participant reactor as reactor (specificClass) + participant engine as kinetics engine (CSTR/PFR) 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, … } + Note over engine: n_iter = floor(speedUpFactor × Δt / timeStep)
each step calls tick(timeStep) + engine->>engine: integrate ASM3 rates (CSTR: Forward Euler / PFR: FD) + engine->>engine: cap S_O to saturation, clip negatives to 0 + engine->>engine: emit 'stateChange' (currentTime) + reactor->>reactor: notifyOutputChanged → getOutput() + reactor->>out: getOutput() → {flow_total, temperature, S_O … X_TS} + alt PFR engine + reactor->>out: GridProfile { grid[n_x][13], n_x, d_x, length, species } end - out->>downstream: Fluent envelope -``` + out->>downstream: Fluent { inlet=0, F, C[13] } via stateChange listener +~~~ -`stateChange` re-emits on `reactor.emitter` (BaseDomain emitter) so downstream reactors / settlers can listen. The effluent emission goes through the BaseNodeAdapter tick pipeline. +`stateChange` re-emits on `reactor.emitter` (BaseDomain emitter) — wired in `specificClass.configure()`. Downstream settlers or chained reactors subscribed via `_connectReactor` call their own `updateState` on each `stateChange` event. The tick loop is opt-in (tick-driven via `static tickInterval`) because the reactor integrates process-time steps that have no fixed wall-clock mapping. ## 8. Data model — `getOutput()` @@ -196,25 +205,27 @@ Species ordering follows ASM3: indices 0–6 are soluble, 7–12 are particulate ## 9. Configuration — editor form ↔ config keys -```mermaid +~~~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] + subgraph editor["Node-RED editor form (reactor.html)"] + f1["Reactor type: CSTR / PFR"] + f2["Volume (m³)"] + f3["Length (m) + Resolution — PFR only"] + f4["Alpha α (boundary condition blend)"] + f5["Number of inlets"] + f6["kLa (d⁻¹) — internal aeration"] + f7["13 × initial concentration fields"] + f8["Time step (s label) + Speed-up factor"] end - subgraph config["Domain config slice"] + subgraph config["Domain config slice (reactor.json)"] c1[reactor.reactor_type] c2[reactor.volume] - c3[reactor.length
reactor.resolution_L] + c3["reactor.length
reactor.resolution_L"] c4[reactor.alpha] - c5[reactor.kla] - c6[reactor.timeStep
reactor.speedUpFactor] - c7[initialState.* ASM3 keys] + c5[reactor.n_inlets] + c6[reactor.kla] + c7["initialState.S_O … X_TS"] + c8["reactor.timeStep (unit: h per schema)
reactor.speedUpFactor"] end f1 --> c1 f2 --> c2 @@ -223,22 +234,24 @@ flowchart TB f5 --> c5 f6 --> c6 f7 --> c7 -``` + f8 --> c8 +~~~ -| Form field | Config key | Default | Range | Where used | +| Form field | Config key | Schema default | Range | Where used | |---|---|---|---|---| -| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` | engine selection in `_buildEngine` | +| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` (schema validator lowercases; `_buildEngine` toUpperCase guards) | engine selection in `Reactor._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 | +| Resolution | `reactor.resolution_L` | `10` | ≥ 1 | PFR grid cell count `n_x` | +| Alpha | `reactor.alpha` | `0.5` | 0–1 | Danckwerts (0) vs Dirichlet (1) inlet BC | | 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 | +| kLa (d⁻¹) | `reactor.kla` | `0` | ≥ 0; set to `NaN` to use `data.otr` instead | `_calcOTR()` in `baseEngine.js` | +| Time step | `reactor.timeStep` | `0.001` | ≥ 0.0001 | integrator inner step (schema says `h`; HTML label says `s` — see limitation #6) | +| Speed-up factor | `reactor.speedUpFactor` | `1` | ≥ 1 | `n_iter = floor(speedUpFactor × Δt_wall / timeStep_days)` | +| Initial S_O | `initialState.S_O` | `0` | ≥ 0 (mg/L) | starting dissolved oxygen (caps to saturation in first tick) | | 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_A | `initialState.X_A` | `200` | ≥ 0 (mg/L) | starting autotroph biomass — must be ≥ ~50 mg/L for nitrification; HTML default is `0.001` (footgun) | | Initial X_TS | `initialState.X_TS` | `3500` | ≥ 0 (mg/L) | starting TSS — drives settler split | ## 10. State chart @@ -278,8 +291,10 @@ One screenshot per tier where helpful. PNG ≤ 200 KB under `wiki/_partial-scree | # | 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` | +| 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. Two remedies tracked: tree-shake mathjs to used ops only; cache the instance. | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" | +| 2 | `initialState.X_A` HTML default is `0.001` mg/L (silently disabling nitrification) but the schema default is `200` mg/L. Always check the deployed node's form value before expecting nitrification. | `reactor.html` line 38 vs `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 | +| 6 | `reactor_type` enum casing: the JSON schema validator lowercases the user-supplied value (`'PFR'` → `'pfr'`). `Reactor._buildEngine` calls `.toUpperCase()` to work around this until Phase 7 decides the platform-wide canonical casing. If the guard is removed prematurely, PFR config silently falls back to CSTR. | `.claude/refactor/OPEN_QUESTIONS.md` — "reactor schema enum lowercases reactor_type" | +| 7 | `timeStep` unit mismatch: the HTML form label says "Time step [s]" but `reactor.json` declares `unit: "h"`. `baseEngine.js` converts `config.timeStep` by `÷ 86 400` (seconds → days), suggesting the true input unit is seconds. Audited in OPEN_QUESTIONS.md Phase 5/6 cleanup list. | `baseEngine.js` line 40; `reactor.json` `timeStep.rules.unit`; `reactor.html` time-step label |