style: palette swatch → (domain-hue redesign 2026-05-21)

Sidebar swatch now follows function family rather than S88 level, so the
palette is visually identifiable instead of monochromatically blue. Editor-group
rectangles in flow.json still follow S88 — only the registerType color changed.
Full table + rationale: superproject .claude/rules/node-red-flow-layout.md §10.0
and .claude/refactor/OPEN_QUESTIONS.md (2026-05-21 entry).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

CLAUDE.md

@@ -21,3 +21,20 @@ Key points for this node:
 - Stack same-level siblings vertically.
 - Parent/children sit on adjacent lanes (children one lane left, parent one lane right).
 - Wrap in a Node-RED group box coloured `#50a8d9` (Unit).
+
+## Folder & File Layout
+
+Every per-node file MUST use the folder name (`reactor`) **exactly**, case-sensitive. Full rule: [`.claude/rules/node-architecture.md`](https://gitea.wbd-rd.nl/RnD/EVOLV/src/branch/development/.claude/rules/node-architecture.md) in the EVOLV superproject.
+
+| Path | Required name |
+|---|---|
+| Entry file | `reactor.js` |
+| Editor HTML | `reactor.html` |
+| Node adapter | `src/nodeClass.js` |
+| Domain logic | `src/specificClass.js` |
+| Editor JS modules | `src/editor/*.js` (extract when inline editor JS exceeds ~50 lines) |
+| Tests | `test/{basic,integration,edge}/*.test.js` |
+| Example flows | `examples/*.flow.json` |
+
+
+When adding new files, read the rule above first to avoid drift.

CONTRACT.md

@@ -3,6 +3,28 @@
 Hand-maintained for Phase 6; the `## Inputs` table is generated from
 `src/commands/index.js` (see Phase 9 generator). Keep ≤ 80 lines.
 
+## Unit convention — approved exception to the canonical-unit rule
+
+EVOLV's canonical units (`CLAUDE.md`, `generalFunctions/CONTRACT.md`)
+are Pa / m³/s / W / K. **reactor diverges deliberately** — it follows
+the ASM (Activated Sludge Model) kinetics literature convention:
+
+- Concentrations: `mg/L` (= g/m³), `mmol/L` for alkalinity.
+- Flow internally: `m³/d` (engine integrator runs in days; see
+  `baseEngine.js` line 40 — `timeStep` config field is seconds, but the
+  internal time base is days).
+- Temperature: `°C`.
+- KLa: `1/h` per the schema; multiplied by the seconds-input `timeStep`
+  inside `_calcOTR` — readers verifying the math should account for the
+  day-internal time base.
+
+Unit conversion at the parent/child boundary happens via
+`MeasurementContainer.UnitPolicy` and the `convert` utility. Other
+nodes (rotatingMachine, pumpingStation, …) honour canonical units;
+reactor is the only ASM-modelled node and pays the small cost of
+domain-textbook units to stay aligned with every published reactor
+reference.
+
 ## Inputs (msg.topic on Port 0)
 
 | Canonical | Aliases (deprecated) | Payload | Effect |

reactor.html

@@ -13,7 +13,7 @@
 <script type="text/javascript">
     RED.nodes.registerType("reactor", {
         category: "EVOLV",
-        color: "#50a8d9",
+        color: "#6FAE5F",
         defaults: {
             name: { value: "" },
             reactor_type: { value: "CSTR", required: true },
@@ -35,7 +35,7 @@
             X_S_init: { value: 75., required: true },
             X_H_init: { value: 30., required: true },
             X_STO_init: { value: 0., required: true },
-            X_A_init: { value: 0.001, required: true },
+            X_A_init: { value: 200, required: true },
             X_TS_init: { value: 125.0009, required: true },
 
             timeStep: { value: 1, required: true },
@@ -267,7 +267,8 @@
         <label for="node-input-dbaseOutputFormat"><i class="fa fa-database"></i> Database Output</label>
         <select id="node-input-dbaseOutputFormat" style="width:60%;">
             <option value="influxdb">influxdb</option>
-            <option value="json">json</option>
+            <option value="frost">frost</option>
+      <option value="json">json</option>
             <option value="csv">csv</option>
         </select>
     </div>

test/basic/timestep-units.basic.test.js

@@ -0,0 +1,44 @@
+'use strict';
+
+// Locks in the contract that `config.timeStep` is interpreted as SECONDS by
+// the reactor kinetics engine. Before 2026-05-19 the schema labelled the field
+// `unit: "h"` while reactor.html labelled it `[s]` and baseEngine divided by
+// 86400 (seconds-per-day) to convert to internal days. A 0.001 schema default
+// — read as hours — would have produced a 3.6 s step; read as seconds it is a
+// 1 ms step. The fix aligned the schema to seconds. This test prevents the
+// drift from reappearing.
+
+const test = require('node:test');
+const assert = require('node:assert/strict');
+
+const { Reactor_CSTR } = require('../../src/specificClass');
+const { makeReactorConfig } = require('../helpers/factories');
+
+const SECONDS_PER_DAY = 24 * 60 * 60;
+
+function makeEngine(timeStepSeconds) {
+  return new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1, timeStep: timeStepSeconds }));
+}
+
+test('engine stores timeStep in days, treating input as seconds', () => {
+  const eng = makeEngine(1);
+  assert.ok(Math.abs(eng.timeStep - 1 / SECONDS_PER_DAY) < 1e-15,
+    `engine.timeStep should be 1/86400 days for a 1-second config; got ${eng.timeStep}`);
+});
+
+test('engine timeStep scales linearly with config.timeStep (seconds in)', () => {
+  const a = makeEngine(1);
+  const b = makeEngine(10);
+  assert.ok(Math.abs(b.timeStep - 10 * a.timeStep) < 1e-15,
+    'engine.timeStep must scale linearly with config.timeStep; broke the seconds→days conversion');
+});
+
+test('schema default for timeStep matches the seconds convention', () => {
+  const path = require('node:path');
+  const gfRoot = path.dirname(require.resolve('generalFunctions'));
+  const schema = require(path.join(gfRoot, 'src/configs/reactor.json'));
+  assert.equal(schema.reactor.timeStep.rules.unit, 's',
+    'schema timeStep.unit must be "s" — engine treats input as seconds');
+  assert.equal(schema.reactor.timeStep.default, 1,
+    'schema timeStep.default must be 1 (1 second), matching reactor.html');
+});

test/helpers/factories.js

@@ -21,7 +21,7 @@ function makeUiConfig(overrides = {}) {
     X_S_init: 75,
     X_H_init: 30,
     X_STO_init: 0,
-    X_A_init: 0.001,
+    X_A_init: 200,
     X_TS_init: 125,
     timeStep: 1,
     enableLog: false,

wiki/Home.md

@@ -1,285 +1,182 @@
 # 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.
+![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue) ![s88](https://img.shields.io/badge/S88-Unit-50a8d9) ![status](https://img.shields.io/badge/status-pending--review-orange)
 
-## 1. What this node is
+A `reactor` models a single biological-treatment tank governed by the ASM3 (Activated Sludge Model No. 3) kinetics. It wraps either a CSTR (fully-mixed) or PFR (plug-flow with axial dispersion) integrator, accepts an influent stream + aeration rate, integrates the 13 ASM3 species each tick, and emits the effluent vector for the next Unit downstream (typically a `settler` or another `reactor`). A `diffuser` (Equipment Module) supplies aeration via `data.otr`; `measurement` children supply temperature and (PFR-only) dissolved-oxygen reconciliation.
 
-**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.
+> [!NOTE]
+> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
 
-## 2. Position in the platform
+---
+
+## At a glance
+
+| Thing | Value |
+|:---|:---|
+| What it represents | One biological-treatment tank running ASM3 kinetics — aerated, anoxic, or anaerobic |
+| S88 level | Unit |
+| Use it when | You need an activated-sludge tank with nitrification / denitrification / heterotrophic growth modelled species-by-species |
+| Don't use it for | Passive equalisation tanks (no reactions), simple residence-time delays (lighter buffer is better), aerobic-only contactors where ASM3's full 13-species vector is overkill |
+| Children it accepts | `measurement` (temperature at equipment; PFR also: dissolved oxygen at numeric distance); upstream `reactor` |
+| Parents / sinks it talks to | downstream `reactor` or `settler` (via `Fluent` on Port 0); `diffuser` pushes `data.otr` in |
+
+---
+
+## How it fits
 
 ```mermaid
 flowchart LR
     upstream[reactor<br/>upstream<br/>Unit]:::unit
-    reactor[reactor<br/>Unit]:::unit
+    rx[reactor<br/>Unit]:::unit
     settler[settler<br/>downstream<br/>Unit]:::unit
-    pump[rotatingMachine<br/>downstream<br/>Equipment]:::equip
-    tsens[measurement<br/>temperature<br/>atequipment]:::ctrl
-    osens[measurement<br/>oxygen<br/>position]:::ctrl
+    diffuser[diffuser<br/>Equipment]:::equip
+    tsens[measurement<br/>temperature<br/>atEquipment]:::ctrl
+    osens[measurement<br/>quantity (oxygen)<br/>at numeric distance, PFR only]:::ctrl
+
+    upstream -.stateChange.-> rx
+    rx -->|Fluent inlet=0| settler
+    diffuser -->|data.otr| rx
+    tsens -.measured.-> rx
+    osens -.measured.-> rx
+    tsens -->|child.register| rx
+    osens -->|child.register| rx
+    upstream -->|child.register<br/>positionVsParent=upstream| rx
 
-    upstream -.stateChange.-> reactor
-    reactor -->|Fluent inlet=0| settler
-    pump -->|child.register downstream| reactor
-    tsens -->|temperature.measured.atequipment| reactor
-    osens -->|quantity (oxygen).measured.&lt;position&gt;| 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`.
+S88 colours are anchored in `.claude/rules/node-red-flow-layout.md`.
 
-## 3. Capability matrix
+reactor sits on lane **L4** (Unit). The `diffuser` (lane L3) is **not** a registered child &mdash; it just pushes aeration via the `data.otr` topic. A reactor chain (multi-stage treatment, e.g. anoxic &rarr; aerobic &rarr; aerobic) is built by registering each upstream reactor with `positionVsParent: 'upstream'`; downstream reactors then `getEffluent` from the upstream on every `stateChange`.
 
-| 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.<distance>` 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
+## Try it &mdash; 3-minute demo
 
-```mermaid
-flowchart TB
-    subgraph nodeRED["nodeClass.js — adapter (BaseNodeAdapter)"]
-        nc["buildDomainConfig()<br/>static DomainClass = Reactor<br/>static commands"]
-    end
-    subgraph domain["specificClass.js — orchestrator (BaseDomain)"]
-        sc["Reactor.configure()<br/>flatten config → build engine<br/>ChildRouter rules"]
-    end
-    subgraph kinetics["src/kinetics/"]
-        be["baseEngine.js<br/>shared ASM3 rate vector"]
-        cstr["cstr.js<br/>0-D integrator"]
-        pfr["pfr.js<br/>spatial discretization + dispersion"]
-    end
-    subgraph commands["src/commands/"]
-        cmds["index.js + handlers.js<br/>6 input topics"]
-    end
-    sc --> be
-    sc --> cstr
-    sc --> pfr
-    nc --> sc
-    nc --> cmds
+Import the basic example flow, deploy, and watch a CSTR consume influent over the simulation clock.
+
+```bash
+curl -X POST -H 'Content-Type: application/json' \
+  --data @nodes/reactor/examples/basic.flow.json \
+  http://localhost:1880/flow
 ```
 
-| 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. |
+What to click after deploy (each inject maps one-to-one to a topic in [Reference &mdash; Contracts](Reference-Contracts#topic-contract)):
 
-## 5. Topic contract
+1. `data.fluent` &mdash; inject an influent stream `{inlet: 0, F: 1000, C: [...13 species...]}` (m³/d, mg/L). The 13 species follow ASM3 ordering.
+2. `data.temperature` &mdash; set reactor temperature (default 20 &deg;C; nitrification rates depend on this).
+3. `data.otr` (if `kla` is `NaN`) **or** rely on the configured `kla` for internal aeration.
+4. `data.clock` &mdash; push wall-clock `msg.timestamp` to advance the integrator. The engine computes `n_iter = floor(speedUpFactor &times; &Delta;t_wall / timeStep_days)` internal Euler / FD steps and integrates them in one shot.
+5. Watch Port 0 (`Fluent` envelope on every advance) and Port 1 (InfluxDB scalar fields: `flow_total`, `temperature`, `S_O`&hellip;`X_TS`).
 
-> **Auto-generated** from `src/commands/index.js`. Do NOT hand-edit between the markers. Re-run `npm run wiki:contract`.
+> [!IMPORTANT]
+> **GIF needed.** Demo recording of steps 1&ndash;5 with `S_NH` falling and `S_NO` rising (nitrification proceeding). Save as `wiki/_partial-gifs/reactor/01-basic-cstr.gif`, target &le; 1&nbsp;MB after `gifsicle -O3 --lossy=80`.
 
-<!-- BEGIN AUTOGEN: topic-contract -->
+---
 
-| Canonical topic | Aliases | Payload | Unit | Effect |
-|---|---|---|---|---|
-| `data.clock` | `clock` | `any` | — | Push the simulation clock tick (timestamp / dt) to the ASM solver. |
-| `data.fluent` | `Fluent` | `object` | — | Push the influent stream (payload: {F: flow m3/h, C: [concentrations mg/L]}). |
-| `data.otr` | `OTR` | `any` | — | Push the current oxygen-transfer rate into the reactor. |
-| `data.temperature` | `Temperature` | `any` | — | Push the current reactor temperature. |
-| `data.dispersion` | `Dispersion` | `any` | — | Push a dispersion/mixing parameter update. |
-| `child.register` | `registerChild` | `any` | — | Register a child node (settler / measurement) with this reactor. |
+## The six things you'll send
 
-<!-- END AUTOGEN: topic-contract -->
+| Topic | Aliases | Payload | What it does |
+|:---|:---|:---|:---|
+| `data.clock` | `clock` | `{timestamp: ms}` (or use `msg.timestamp`) | Advance the integrator. `updateState` computes how many internal steps fit between `currentTime` and the supplied timestamp (scaled by `speedUpFactor`) and runs them. |
+| `data.fluent` | `Fluent` | `{inlet: number, F: number, C: number[13]}` | Set the per-inlet flow rate (`F`) and concentration vector (`C`). Stored in `engine.Fs[inlet]` / `engine.Cs_in[inlet]`. |
+| `data.otr` | `OTR` | numeric | Set the externally-supplied oxygen transfer rate. Used when `kla` is `NaN`; ignored otherwise (internal mass transfer takes over). |
+| `data.temperature` | `Temperature` | numeric or `{value: number}` | Set `engine.temperature` (&deg;C). Non-numeric payloads are warned and ignored. |
+| `data.dispersion` | `Dispersion` | numeric | **PFR only** &mdash; set axial dispersion coefficient `D` (m²/d). Triggers Peclet / Courant guard warnings on the next `updateState`. |
+| `child.register` | `registerChild` | child node id (string) | Register a sibling node (`measurement`, upstream `reactor`) with this reactor. Port 2 wiring does this automatically in normal flows. |
 
-## 6. Child registration
+> [!NOTE]
+> Pending full node review (2026-05). reactor's command surface is data-push only &mdash; there is **no FSM, no setpoint, no mode**. The kinetics engine runs continuous-state ODE / PDE integration; the only stateful event is `stateChange` after every successful advance.
 
-```mermaid
-flowchart LR
-    subgraph kids["accepted children (softwareType)"]
-        m_t["measurement<br/>temperature"]:::ctrl
-        m_o["measurement<br/>quantity (oxygen)"]:::ctrl
-        r_up["reactor<br/>upstream"]:::unit
-    end
-    m_t -->|temperature.measured.atEquipment| h_meas[engine._connectMeasurement]
-    m_o -->|quantity (oxygen).measured.&lt;pos&gt;| 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.<distance>` → 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. |
+## What you'll see come out
 
-## 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,<br/>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.
-
-<!-- BEGIN AUTOGEN: data-model -->
-
-| 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` |
-
-<!-- END AUTOGEN: data-model -->
-
-**Concrete sample** (CSTR mid-integration, nitrifying):
+Sample Port 0 message (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
+  "topic": "Fluent",
+  "payload": {
+    "inlet": 0,
+    "F": 1000,
+    "C": [2.1, 30, 12.4, 0.8, 4.3, 18.6, 4.2, 1050, 65, 2150, 4.5, 215, 3680]
+  },
+  "timestamp": 1747500000000
 }
 ```
 
-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.
+The `C` array is the 13-species ASM3 vector in fixed order (indices 0&ndash;6 soluble, 7&ndash;12 particulate). For a PFR an additional message goes out on the same port **before** the effluent each advance:
 
-## 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<br/>reactor.resolution_L]
-        c4[reactor.alpha]
-        c5[reactor.kla]
-        c6[reactor.timeStep<br/>reactor.speedUpFactor]
-        c7[initialState.* ASM3 keys]
-    end
-    f1 --> c1
-    f2 --> c2
-    f3 --> c3
-    f4 --> c4
-    f5 --> c5
-    f6 --> c6
-    f7 --> c7
+```json
+{
+  "topic": "GridProfile",
+  "payload": {
+    "grid": [[...13...], [...13...], "...n_x rows..."],
+    "n_x": 10,
+    "d_x": 1.0,
+    "length": 10,
+    "species": ["S_O","S_I","S_S","S_NH","S_N2","S_NO","S_HCO","X_I","X_S","X_H","X_STO","X_A","X_TS"],
+    "timestamp": 1747500000000
+  }
+}
 ```
 
-| 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 |
+Port 1 (InfluxDB telemetry) carries the same data flattened as scalar fields &mdash; `flow_total` (m³/d), `temperature` (&deg;C), and one field per species (`S_O`, `S_I`, `S_S`, `S_NH`, `S_N2`, `S_NO`, `S_HCO`, `X_I`, `X_S`, `X_H`, `X_STO`, `X_A`, `X_TS`, mg/L; `S_HCO` is mmol/L).
 
-## 10. State chart
+| Field | Meaning |
+|:---|:---|
+| `S_O` | Dissolved oxygen. Capped to saturation at each tick via `_capDissolvedOxygen`. |
+| `S_I` | Inert soluble COD. |
+| `S_S` | Readily biodegradable substrate. |
+| `S_NH` | Ammonium nitrogen. Drops during nitrification. |
+| `S_N2` | Dinitrogen (denitrification end product). |
+| `S_NO` | Nitrate / nitrite nitrogen. Rises during nitrification. |
+| `S_HCO` | Alkalinity (bicarbonate, mmol/L). |
+| `X_I` | Inert particulate COD. |
+| `X_S` | Slowly biodegradable substrate. |
+| `X_H` | Heterotrophic biomass. |
+| `X_STO` | Stored COD in biomass. |
+| `X_A` | Autotrophic biomass. **Must be &ge; ~50 mg/L for nitrification to proceed.** |
+| `X_TS` | Total suspended solids. Drives the downstream settler split. |
+| `flow_total` | Effluent volumetric flow (m³/d) &mdash; `sum(Fs)`. |
+| `temperature` | Reactor temperature (&deg;C). |
 
-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
+## The interesting bits
 
-| 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 |
+### CSTR vs PFR
 
-One screenshot per tier where helpful. PNG ≤ 200 KB under `wiki/_partial-screenshots/reactor/`.
+The engine is selected once at `configure()` from `reactor.reactor_type`. The same input topics drive both, but PFR additionally:
 
-## 12. Debug recipes
+- Discretises the tank along the `length` axis into `resolution_L` grid cells (`n_x`).
+- Emits a `GridProfile` message **before** the effluent each `updateState`.
+- Honours `data.dispersion` to set the axial dispersion coefficient.
+- Reconciles oxygen measurements at a **numeric** `positionVsParent` (interpreted as distance from inlet) into the nearest grid cell.
+- Warns when local Peclet &ge; 2 or Courant &ge; 0.5 (stability of the explicit FD scheme).
 
-| 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` |
+Hot-swapping engine type at runtime is not supported &mdash; redeploy the flow.
 
-## 13. When you would NOT use this node
+### Aeration: internal `kla` vs external `data.otr`
 
-- 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`.
+`reactor.kla > 0` enables internal mass-transfer: `OTR = kla &times; (sat(T) &minus; S_O)`. Set `kla = NaN` to fall through to the externally-pushed `data.otr` value (the path a `diffuser` Equipment node uses).
 
-## 14. Known limitations / current issues
+### `X_A` footgun
 
-| # | 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 |
+The HTML editor form's default initial autotroph biomass is `0.001` mg/L &mdash; effectively zero, so nitrification never starts. The JSON schema default is `200` mg/L. Always check the deployed node's form value before expecting `S_NH` to drop. See [Reference &mdash; Limitations](Reference-Limitations#x_a-initial-default-footgun).
+
+---
+
+## Need more?
+
+| Page | What you'll find |
+|:---|:---|
+| [Reference &mdash; Contracts](Reference-Contracts) | Full topic contract, config schema, child registration filters |
+| [Reference &mdash; Architecture](Reference-Architecture) | Code map, integration sequence, kinetics layout, output ports |
+| [Reference &mdash; Examples](Reference-Examples) | Shipped example flows + debug recipes |
+| [Reference &mdash; Limitations](Reference-Limitations) | When not to use, known limitations, open questions |
+
+[EVOLV master wiki](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Home) &middot; [Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns) &middot; [Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions)

wiki/Reference-Architecture.md

@@ -0,0 +1,293 @@
+# Reference — Architecture
+
+![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
+
+> [!NOTE]
+> Code structure for `reactor`: the three-tier sandwich, the `src/` layout, the ASM3 kinetics engines (CSTR + PFR), the integration sequence, child registration, and the output-port pipeline. For an intuitive overview, return to [Home](Home).
+>
+> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
+
+---
+
+## Three-tier code layout
+
+```
+nodes/reactor/
+|
++-- reactor.js                     entry: RED.nodes.registerType('reactor', NodeClass)
+|
++-- src/
+|     nodeClass.js                 extends BaseNodeAdapter (Node-RED bridge)
+|     specificClass.js             extends BaseDomain (orchestration only)
+|     utils.js                     assertNoNaN + small helpers
+|     |
+|     +-- commands/
+|     |     index.js               6 topic descriptors
+|     |     handlers.js            pure handler functions
+|     |
+|     +-- kinetics/
+|     |     baseEngine.js          BaseReactorEngine (influent / OTR / T / child wiring / updateState)
+|     |     cstr.js                Reactor_CSTR extends BaseReactorEngine (0-D Forward Euler)
+|     |     pfr.js                 Reactor_PFR  extends BaseReactorEngine (axial FD + Danckwerts BC)
+|     |
+|     +-- reaction_modules/
+|     |     asm3_class.js          ASM3 stoichiometry + rate vector + species list
+|     |     asm3_class Koch.js     legacy variant (not consumed by current engines)
+|     |
+|     +-- io/                      reserved (currently empty)
+|
++-- additional_nodes/
+|     recirculation-pump.{js,html} legacy companion node shipped from this repo
+|     settling-basin.{js,html}     legacy companion node shipped from this repo
+```
+
+### Tier responsibilities
+
+| Tier | File | What it owns | Touches `RED.*` |
+|:---|:---|:---|:---:|
+| entry | `reactor.js` | Type registration | Yes |
+| nodeClass | `src/nodeClass.js` | Tick loop (`tickInterval = 1000` ms), status badge (`statusInterval = 1000` ms), `buildDomainConfig` mapping editor fields to nested config, `_emitOutputs` override that preserves the `Fluent` + `GridProfile` envelope (BaseNodeAdapter's default delta-compressed payload doesn't fit). | Yes |
+| specificClass | `src/specificClass.js` | `_flattenEngineConfig` translates nested schema to engine shape; `_buildEngine` selects CSTR or PFR; wires ChildRouter (`measurement` → `engine._connectMeasurement`, `reactor` → `engine._connectReactor`); re-emits engine `stateChange` on the BaseDomain emitter; surfaces `getOutput()`, `getStatusBadge()`. | No |
+| kinetics | `src/kinetics/*.js` | Pure ASM3 integration. `BaseReactorEngine` owns influent state, OTR, temperature, child-registration utils, and `updateState`. `Reactor_CSTR` adds the 0-D Forward-Euler tick. `Reactor_PFR` adds spatial discretization + boundary conditions + grid-profile emission. | No |
+
+`specificClass` is thin stitching. All the real work lives in the kinetics engines.
+
+---
+
+## No FSM — continuous-state integration
+
+reactor has **no finite-state machine, no mode, no setpoint**. The engine runs continuous ODE / PDE integration in process time. The only stateful event is `stateChange`, emitted by `BaseReactorEngine.updateState` after every successful advance (`n_iter > 0` internal steps completed).
+
+```mermaid
+flowchart LR
+    clk[data.clock<br/>or tick&#40;dt&#41;]:::input --> us[updateState&#40;newTime&#41;]
+    us --> ni{n_iter = floor&#40;<br/>speedUpFactor &times; &Delta;t / timeStep&#41;}
+    ni -->|0| skip[no-op]
+    ni -->|>0| loop[for each step:<br/>tick&#40;timeStep&#41;]
+    loop --> emit[emit stateChange&#40;currentTime&#41;]
+    classDef input fill:#a9daee,color:#000
+```
+
+`stateChange` is the trigger downstream Units (settlers, chained reactors) use to pull effluent.
+
+---
+
+## Kinetics engines &mdash; CSTR vs PFR
+
+```mermaid
+flowchart TB
+    subgraph base["BaseReactorEngine"]
+        bs["Fs[], Cs_in[][13]<br/>OTR, temperature, kla<br/>upstreamReactor link<br/>updateState&#40;newTime&#41;<br/>_connectMeasurement / _connectReactor"]
+    end
+    subgraph cstr["Reactor_CSTR"]
+        cs["state = number[13]<br/>tick&#40;dt&#41;:<br/>  inflow + outflow + reaction + transfer<br/>  Forward Euler<br/>  _capDissolvedOxygen / _arrayClip2Zero"]
+    end
+    subgraph pfr["Reactor_PFR"]
+        ps["state = number[n_x][13]<br/>length, n_x, d_x, A, alpha, D<br/>D_op / D2_op finite-difference operators<br/>tick&#40;dt&#41;:<br/>  dispersion + advection + reaction + transfer<br/>  Explicit FD<br/>  Danckwerts inlet / Neumann outlet BC<br/>  Peclet / Courant guard warnings"]
+    end
+    bs --> cs
+    bs --> ps
+```
+
+### Forward Euler (CSTR)
+
+`Reactor_CSTR.tick(time_step)` adds four contributions per step:
+
+| Term | Formula | Notes |
+|:---|:---|:---|
+| Inflow | `Fs &middot; Cs_in / volume` | Per inlet, summed into a single concentration delta. |
+| Outflow | `&minus;sum(Fs) / volume &middot; state` | Mass leaves at the current tank concentration. |
+| Reaction | `asm.compute_dC(state, T)` | ASM3 rate vector applied at current temperature. |
+| Transfer | `OTR or kla &middot; (sat(T) &minus; S_O)` on the `S_O` index only | All other species: zero transfer. |
+
+After integration, `_capDissolvedOxygen` caps `S_O` to saturation and `_arrayClip2Zero` floors negative concentrations.
+
+### Explicit FD (PFR)
+
+`Reactor_PFR.tick(time_step)` operates per grid cell:
+
+| Term | Notes |
+|:---|:---|
+| Dispersion | `(D / d_x²) &middot; D2_op &middot; state` &mdash; central-difference second-derivative operator. |
+| Advection | `(&minus;sum(Fs) / (A &middot; d_x)) &middot; D_op &middot; state` &mdash; first-derivative operator (central or upwind per config). |
+| Reaction | Per-cell `asm.compute_dC(slice, T)`. |
+| Transfer | OTR / `kla` on the `S_O` index, scaled by `n_x / (n_x &minus; 2)` for interior cells only. |
+
+Boundary conditions: **Danckwerts** at the inlet when `sum(Fs) > 0` (mixes inlet concentration with diffusive back-mix governed by `alpha`); **Neumann** (no-flux) at the outlet and at the inlet when there is no flow. After integration, the same `_capDissolvedOxygen` / `_arrayClip2Zero` post-processing applies cell-by-cell.
+
+`updateState` extends `BaseReactorEngine.updateState` with two stability checks:
+
+| Check | Threshold | Warning |
+|:---|:---|:---|
+| Local Peclet `Pe = d_x &middot; sum(Fs) / (D &middot; A)` | `&ge; 2` | `Local Peclet number (&hellip;) is too high! Increase reactor resolution.` |
+| Courant `Co_D = D &middot; timeStep / d_x²` | `&ge; 0.5` | `Courant number (&hellip;) is too high! Reduce time step size.` |
+
+---
+
+## Lifecycle &mdash; what one `data.clock` advance does
+
+```mermaid
+sequenceDiagram
+    autonumber
+    participant clock as data.clock injector
+    participant rx as reactor (specificClass)
+    participant engine as kinetics engine (CSTR / PFR)
+    participant downstream as settler / next reactor
+    participant out as Port 0 / 1
+
+    clock->>rx: data.clock { timestamp }
+    rx->>engine: updateState(timestamp)
+    Note over engine: n_iter = floor(speedUpFactor &times; &Delta;t / timeStep)
+    alt upstreamReactor present
+        engine->>engine: setInfluent = upstream.getEffluent
+    end
+    loop n_iter times
+        engine->>engine: tick(timeStep) &mdash; integrate ASM3 rates
+        engine->>engine: cap S_O to saturation, clip negatives
+    end
+    engine->>rx: emit 'stateChange' (currentTime)
+    rx->>rx: re-emit 'stateChange' on BaseDomain emitter
+    rx->>rx: notifyOutputChanged
+    alt PFR engine
+        rx->>out: Port 0 &mdash; GridProfile { grid, n_x, d_x, length, species }
+    end
+    rx->>out: Port 0 &mdash; Fluent { inlet=0, F, C[13] }
+    rx->>out: Port 1 &mdash; InfluxDB scalars { flow_total, temperature, S_O&hellip;X_TS }
+    downstream-->>rx: subscribes to stateChange via _connectReactor
+    downstream->>downstream: pulls getEffluent on each stateChange
+```
+
+The tick loop is opt-in (`static tickInterval = 1000`) because the integrator advances **process time** in steps that have no fixed wall-clock mapping. Without ticks the engine simply doesn't advance. `nodeClass._emitOutputs` is overridden so the `Fluent` / `GridProfile` envelope shape survives the BaseNodeAdapter pipeline.
+
+---
+
+## Child registration
+
+Source: `src/specificClass.js` `configure()` wires the ChildRouter; `BaseReactorEngine._connectMeasurement` and `_connectReactor` do the actual subscription.
+
+```mermaid
+flowchart LR
+    subgraph kids["accepted children (softwareType)"]
+        m_t["measurement<br/>asset.type=temperature<br/>positionVsParent=atEquipment"]:::ctrl
+        m_o["measurement<br/>asset.type=quantity (oxygen)<br/>positionVsParent=numeric distance (PFR)"]:::ctrl
+        r_up["reactor<br/>positionVsParent=upstream"]:::unit
+    end
+    m_t -->|temperature.measured.atEquipment| h_meas["engine._connectMeasurement<br/>(baseEngine.js)"]
+    m_o -->|quantity(oxygen).measured.&lt;distance&gt;| h_meas
+    r_up -.stateChange.-> h_react["engine._connectReactor<br/>(baseEngine.js)"]
+    h_meas --> reconcile["reconcile T &rarr; engine.temperature<br/>reconcile O2 &rarr; state grid cell (PFR only)"]
+    h_react --> pull["pull upstream getEffluent<br/>&rarr; Fs[0] / Cs_in[0] before next tick"]
+    classDef ctrl fill:#a9daee,color:#000
+    classDef unit fill:#50a8d9,color:#000
+```
+
+### `_connectMeasurement` event wiring
+
+`measurement.measurements.emitter` fires `<measurementType>.measured.<position>` on every published value. The reactor subscribes:
+
+```js
+const eventName = `${measurementType}.measured.${position}`;
+measurement.measurements.emitter.on(eventName, (eventData) => {
+  this.measurements
+    .type(measurementType).variant('measured').position(position)
+    .value(eventData.value, eventData.timestamp, eventData.unit);
+  this._updateMeasurement(measurementType, eventData.value, position, eventData);
+});
+```
+
+`_updateMeasurement` (CSTR base): only `temperature` at `POSITIONS.AT_EQUIPMENT` is honoured &mdash; writes `engine.temperature`. Any other type logs `Type '<x>' not recognized for measured update.`
+
+`_updateMeasurement` (PFR override): additionally handles `quantity (oxygen)` at a **numeric** position. Position is interpreted as metres along `length`; the value is written to grid cell `clamp(round(pos / length &times; n_x), 0, n_x &minus; 1)`. Non-finite position / value, or `length &le; 0`, logs a warn and the update is dropped.
+
+### `_connectReactor` &mdash; upstream chain
+
+Setting `positionVsParent: 'upstream'` on the upstream reactor's child-register makes this reactor subscribe to the upstream's `stateChange`. On every event the downstream's `updateState` runs, which first pulls the upstream's `getEffluent` into `Fs[0]` / `Cs_in[0]` then integrates.
+
+> [!NOTE]
+> `diffuser` is **not** a registered child. It feeds aeration via the `data.otr` topic on Port 0 (handled in `commands/handlers.js` `dataOTR`). No child-registration handshake.
+
+---
+
+## Output ports
+
+| Port | Carries | Sample shape |
+|:---|:---|:---|
+| 0 (process) | `Fluent` envelope every advance. For PFR: an additional `GridProfile` message sent **before** the `Fluent`. | `{topic: 'Fluent', payload: {inlet: 0, F, C: [...13...]}, timestamp}` |
+| 1 (telemetry) | InfluxDB line-protocol payload built from `getOutput()` via `outputUtils.formatMsg`. Fields: `flow_total`, `temperature`, and one per species. | `reactor,id=rx_a flow_total=1000,temperature=20,S_O=2.1,S_NH=0.8,...` |
+| 2 (registration) | `child.register` upward at init | `{topic: 'child.register', payload: <node.id>, positionVsParent, distance}` |
+
+<!-- BEGIN AUTOGEN: data-model — populate via wiki-gen tool (TODO) -->
+
+> [!NOTE]
+> Pending full node review (2026-05). The flat Port-1 telemetry shape (one field per species, plus `flow_total` + `temperature`) reflects the current `getOutput()` in `src/specificClass.js`.
+
+| Key | Type | Unit | Source |
+|:---|:---|:---|:---|
+| `flow_total` | number | m³/d | `sum(Fs)` from the engine's effluent envelope |
+| `temperature` | number | &deg;C | `engine.temperature` |
+| `S_O` | number | mg/L | effluent `C[0]` &mdash; dissolved oxygen, capped to saturation |
+| `S_I` | number | mg/L | effluent `C[1]` &mdash; inert soluble COD |
+| `S_S` | number | mg/L | effluent `C[2]` &mdash; readily biodegradable substrate |
+| `S_NH` | number | mg/L | effluent `C[3]` &mdash; ammonium nitrogen |
+| `S_N2` | number | mg/L | effluent `C[4]` &mdash; dinitrogen |
+| `S_NO` | number | mg/L | effluent `C[5]` &mdash; nitrate / nitrite |
+| `S_HCO` | number | mmol/L | effluent `C[6]` &mdash; alkalinity |
+| `X_I` | number | mg/L | effluent `C[7]` &mdash; inert particulate COD |
+| `X_S` | number | mg/L | effluent `C[8]` &mdash; slowly biodegradable substrate |
+| `X_H` | number | mg/L | effluent `C[9]` &mdash; heterotrophic biomass |
+| `X_STO` | number | mg/L | effluent `C[10]` &mdash; stored COD in biomass |
+| `X_A` | number | mg/L | effluent `C[11]` &mdash; autotrophic biomass |
+| `X_TS` | number | mg/L | effluent `C[12]` &mdash; total suspended solids |
+
+<!-- END AUTOGEN: data-model -->
+
+### Status badge
+
+Composed by `getStatusBadge()` in `src/specificClass.js`:
+
+```
+<EngineType>  T=<temperature> C  F=<flow> m³/d  S_O=<S_O> mg/L
+```
+
+Engine type is `CSTR` or `PFR` (derived from the constructor name). Fill is green by default; the badge is purely informational &mdash; no shape / colour transitions tied to plant state, since reactor has no FSM.
+
+---
+
+## Event sources
+
+| Source | Where it fires | What it triggers |
+|:---|:---|:---|
+| `engine.emitter` `'stateChange'` | `BaseReactorEngine.updateState` after `n_iter > 0` integration steps | `specificClass` re-emits on `this.emitter`; BaseNodeAdapter `_emitOutputs` runs (Port 0 + Port 1) |
+| Child measurement emitter | `measurement.measurements.emitter` per `<type>.measured.<position>` | `engine._connectMeasurement` callback &rarr; writes into MeasurementContainer + `_updateMeasurement` reconcile |
+| Upstream reactor `'stateChange'` | Upstream reactor's `BaseDomain` emitter | `engine._connectReactor` callback &rarr; downstream `updateState(t)` runs, pulling upstream effluent first |
+| Inbound `msg.topic` | Node-RED input wire | `commandRegistry` dispatch |
+| `setInterval(tickInterval = 1000)` | `BaseNodeAdapter` periodic tick | `nodeClass._emitOutputs` &rarr; `source.updateState(Date.now())` + send |
+| `setInterval(statusInterval = 1000)` | `BaseNodeAdapter` | Status badge re-render |
+
+---
+
+## Where to start reading
+
+| If you're changing&hellip; | Read first |
+|:---|:---|
+| ASM3 stoichiometry / kinetic constants | `src/reaction_modules/asm3_class.js` |
+| Mixed-tank integration, child wiring, influent / OTR / T setters | `src/kinetics/baseEngine.js`, `src/kinetics/cstr.js` |
+| Plug-flow discretization, dispersion, grid profile | `src/kinetics/pfr.js` |
+| Topic registration, alias deprecation | `src/commands/index.js`, `src/commands/handlers.js` |
+| Editor-field &harr; engine-config mapping | `src/nodeClass.js` `buildDomainConfig`, `src/specificClass.js` `_flattenEngineConfig` |
+| Port-0 envelope shape (`Fluent` + `GridProfile`) | `src/nodeClass.js` `_emitOutputs` |
+| Schema defaults, types, units | `generalFunctions/src/configs/reactor.json` |
+
+---
+
+## Related pages
+
+| Page | Why |
+|:---|:---|
+| [Home](Home) | Intuitive overview |
+| [Reference &mdash; Contracts](Reference-Contracts) | Topic + config + child filters |
+| [Reference &mdash; Examples](Reference-Examples) | Shipped flows + debug recipes |
+| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
+| [settler wiki](https://gitea.wbd-rd.nl/RnD/settler/wiki/Home) | The typical downstream Unit that subscribes to reactor `stateChange` |
+| [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home) | The Equipment node that pushes `data.otr` |
+| [EVOLV &mdash; Architecture](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Architecture) | Platform-wide three-tier pattern |

wiki/Reference-Contracts.md

@@ -0,0 +1,227 @@
+# Reference — Contracts
+
+![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
+
+> [!NOTE]
+> Full topic contract, configuration schema, and child-registration filters for `reactor`. Source of truth: `src/commands/index.js`, `src/specificClass.js` `configure()`, and the schema at `generalFunctions/src/configs/reactor.json`.
+>
+> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
+>
+> For an intuitive overview, return to the [Home](Home).
+
+---
+
+## Topic contract
+
+The registry lives in `src/commands/index.js`. Each descriptor maps a canonical `msg.topic` to its handler; aliases emit a one-time deprecation warning the first time they fire.
+
+<!-- BEGIN AUTOGEN: topic-contract -->
+
+| Canonical topic | Aliases | Payload | Unit | Effect |
+|---|---|---|---|---|
+| `data.clock` | `clock` | any | — | Push the simulation clock tick (timestamp / dt) to the ASM solver. |
+| `data.fluent` | `Fluent` | `object` | — | Push the influent stream (payload: {F: flow m3/h, C: [concentrations mg/L]}). |
+| `data.otr` | `OTR` | any | — | Push the current oxygen-transfer rate into the reactor. |
+| `data.temperature` | `Temperature` | any | — | Push the current reactor temperature. |
+| `data.dispersion` | `Dispersion` | any | — | Push a dispersion/mixing parameter update. |
+| `child.register` | `registerChild` | any | — | Register a child node (settler / measurement) with this reactor. |
+
+<!-- END AUTOGEN: topic-contract -->
+
+### Modes / sources / actions
+
+reactor has **no mode, no action allow-lists, no source gating**. All topics are accepted as long as the payload shape is valid. (Contrast with `rotatingMachine`, which gates every input through a mode &times; source matrix.)
+
+---
+
+## Data model &mdash; `getOutput()` shape
+
+Composed each tick by `src/specificClass.js` `getOutput()`. Used to build the Port-1 InfluxDB payload; Port 0 carries the engine's `getEffluent` envelope directly.
+
+### Port-0 process payload
+
+The engine's effluent envelope, emitted on every successful `updateState` advance:
+
+```json
+{
+  "topic": "Fluent",
+  "payload": { "inlet": 0, "F": <m³/d>, "C": [<13 species, mg/L>] },
+  "timestamp": <ms since epoch>
+}
+```
+
+For a PFR an additional message is sent **before** the `Fluent` on the same port each advance:
+
+```json
+{
+  "topic": "GridProfile",
+  "payload": {
+    "grid": [[<13 cells of n_x>]],
+    "n_x": <int>,
+    "d_x": <m>,
+    "length": <m>,
+    "species": ["S_O","S_I","S_S","S_NH","S_N2","S_NO","S_HCO","X_I","X_S","X_H","X_STO","X_A","X_TS"],
+    "timestamp": <ms since epoch>
+  }
+}
+```
+
+### Port-1 telemetry &mdash; scalar keys
+
+| Key | Type | Unit | Source |
+|:---|:---|:---|:---|
+| `flow_total` | number | m³/d | `sum(Fs)` from effluent envelope |
+| `temperature` | number | &deg;C | `engine.temperature` |
+| `S_O` | number | mg/L | effluent `C[0]` &mdash; capped to saturation by `_capDissolvedOxygen` |
+| `S_I` | number | mg/L | effluent `C[1]` |
+| `S_S` | number | mg/L | effluent `C[2]` |
+| `S_NH` | number | mg/L | effluent `C[3]` |
+| `S_N2` | number | mg/L | effluent `C[4]` |
+| `S_NO` | number | mg/L | effluent `C[5]` |
+| `S_HCO` | number | mmol/L | effluent `C[6]` &mdash; alkalinity |
+| `X_I` | number | mg/L | effluent `C[7]` |
+| `X_S` | number | mg/L | effluent `C[8]` |
+| `X_H` | number | mg/L | effluent `C[9]` |
+| `X_STO` | number | mg/L | effluent `C[10]` |
+| `X_A` | number | mg/L | effluent `C[11]` |
+| `X_TS` | number | mg/L | effluent `C[12]` |
+
+Non-finite species values are **omitted** from the output (the `Number.isFinite` guard in `getOutput`); they are not emitted as `null`. Pick one convention per consumer (absent vs null) and document it &mdash; see `.claude/rules/output-coverage.md`.
+
+### Species ordering
+
+The 13-species vector is **fixed**:
+
+| Index | Key | Group |
+|:---:|:---|:---|
+| 0 | `S_O` | soluble |
+| 1 | `S_I` | soluble |
+| 2 | `S_S` | soluble |
+| 3 | `S_NH` | soluble |
+| 4 | `S_N2` | soluble |
+| 5 | `S_NO` | soluble |
+| 6 | `S_HCO` | soluble |
+| 7 | `X_I` | particulate |
+| 8 | `X_S` | particulate |
+| 9 | `X_H` | particulate |
+| 10 | `X_STO` | particulate |
+| 11 | `X_A` | particulate |
+| 12 | `X_TS` | particulate |
+
+Don't reshuffle &mdash; `getOutput()` and `_flattenEngineConfig()` both depend on this exact order, as does `additional_nodes/settling-basin` and the downstream `settler` node.
+
+### Status badge
+
+`getStatusBadge()` in `src/specificClass.js`:
+
+```
+<EngineType>  T=<°C>.X C  F=<m³/d>.XX m³/d  S_O=<mg/L>.XX mg/L
+```
+
+Engine type is the constructor name with `Reactor_` stripped (so `CSTR` or `PFR`). Badge is always green-dot (no FSM-driven state).
+
+---
+
+## Configuration schema &mdash; editor form to config keys
+
+Source of truth: `generalFunctions/src/configs/reactor.json` plus `nodeClass.buildDomainConfig` (`src/nodeClass.js`).
+
+### General (`config.general`)
+
+| Form field | Config key | Default | Notes |
+|:---|:---|:---|:---|
+| Name | `general.name` | `Reactor` | Human-readable. |
+| (auto-assigned) | `general.id` | `null` | Node-RED node id. |
+| Default unit | `general.unit` | `null` | Unused by the reactor's own logic (the engines pick up units from the schema's `rules.unit` strings); kept for parent compatibility. |
+| Log enabled | `general.logging.enabled` | `true` | Master switch. |
+| Log level | `general.logging.logLevel` | `info` | `debug` / `info` / `warn` / `error`. |
+
+### Functionality (`config.functionality`)
+
+| Form field | Config key | Default | Notes |
+|:---|:---|:---|:---|
+| Position vs parent | `functionality.positionVsParent` | `atEquipment` | Used in the child-register payload that goes UP to whatever parent registers this reactor. Enum: `upstream` / `atEquipment` / `downstream`. |
+| (hidden) | `functionality.softwareType` | `reactor` | Constant. |
+| (hidden) | `functionality.role` | `Biological reactor for wastewater treatment` | Constant. |
+
+### Reactor (`config.reactor`)
+
+| Form field | Config key | Schema default | Range / unit | Notes |
+|:---|:---|:---|:---|:---|
+| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` | Selected once at `configure()`. `_buildEngine` calls `.toUpperCase()` so `pfr` and `PFR` both resolve. |
+| Volume | `reactor.volume` | `1000` | m³, `> 0` | Used by mass balance and (PFR) surface-area derivation. |
+| Length | `reactor.length` | `10` | m, `> 0` | **PFR only.** Sets axial extent and grid pitch (`d_x = length / n_x`). |
+| Resolution | `reactor.resolution_L` | `10` | integer `&ge; 1` | **PFR only.** Grid cell count `n_x`. |
+| Alpha | `reactor.alpha` | `0.5` | `0..1` | **PFR only.** Inlet boundary blend: `0` = pure Danckwerts, `1` = fully mixed inlet. |
+| Inlets | `reactor.n_inlets` | `1` | integer `&ge; 1` | `Fs[]` / `Cs_in[]` array size. |
+| kLa | `reactor.kla` | `0` | 1/h, `&ge; 0`; set `NaN` to disable | Enables internal aeration `OTR = kla &middot; (sat(T) &minus; S_O)`. When `NaN`, `data.otr` is honoured instead. |
+| Time step | `reactor.timeStep` | `0.001` | `&ge; 0.0001` | Schema declares unit `h`; `baseEngine.js` converts by `&divide; 86400` (treating it as seconds). See [Limitations &mdash; timeStep unit mismatch](Reference-Limitations#timestep-unit-mismatch). |
+| Speed-up factor | `reactor.speedUpFactor` | `1` | `&ge; 1` | Multiplies wall-clock &Delta;t when computing `n_iter`. `2` means twice as many internal steps per second. |
+
+### Initial state (`config.initialState`)
+
+13 starting concentrations, all written into the engine's `state` (CSTR: single row; PFR: replicated across all `n_x` grid cells at construction).
+
+| Form field | Config key | Schema default | HTML default | Unit | Notes |
+|:---|:---|:---|:---|:---|:---|
+| Initial S_O | `initialState.S_O` | `0` | check editor | mg/L | Capped to saturation on the first tick. |
+| Initial S_I | `initialState.S_I` | `30` | check editor | mg/L | Inert soluble COD. |
+| Initial S_S | `initialState.S_S` | `70` | check editor | mg/L | Readily biodegradable substrate. |
+| Initial S_NH | `initialState.S_NH` | `25` | check editor | mg/L | Ammonium &mdash; declines with nitrification. |
+| Initial S_N2 | `initialState.S_N2` | `0` | check editor | mg/L | Dinitrogen. |
+| Initial S_NO | `initialState.S_NO` | `0` | check editor | mg/L | Nitrate / nitrite. |
+| Initial S_HCO | `initialState.S_HCO` | `5` | check editor | mmol/L | Alkalinity. |
+| Initial X_I | `initialState.X_I` | `1000` | check editor | mg/L | Inert particulate COD. |
+| Initial X_S | `initialState.X_S` | `100` | check editor | mg/L | Slowly biodegradable substrate. |
+| Initial X_H | `initialState.X_H` | `2000` | check editor | mg/L | Heterotrophic biomass. |
+| Initial X_STO | `initialState.X_STO` | `0` | check editor | mg/L | Stored COD in biomass. |
+| Initial X_A | `initialState.X_A` | `200` | **`0.001`** | mg/L | **Footgun.** HTML default in `reactor.html` (per `CONTRACT.md`) is effectively zero, disabling nitrification. Always verify the deployed form value. |
+| Initial X_TS | `initialState.X_TS` | `3500` | check editor | mg/L | Total suspended solids &mdash; drives downstream settler split. |
+
+> [!WARNING]
+> The HTML form supplies its own defaults; for fields where they differ from the schema (notably `X_A`), the HTML wins at deploy time. Either match the schema in the HTML or audit every deployed flow.
+
+### Unit policy
+
+reactor does **not** declare a UnitPolicy in `specificClass`. Units are carried in the schema's `rules.unit` strings (m³, m, 1/h, mg/L, mmol/L) and consumed by the engines without normalisation through MeasurementContainer's canonical-unit rule. Notable internal conversions:
+
+| Quantity | What the engine uses internally | Where converted |
+|:---|:---|:---|
+| `timeStep` | days | `baseEngine.js` line ~40: `timeStep = config.timeStep / 86400` |
+| `Fs` | m³/d (assumed by mass-balance formulas) | not converted &mdash; the caller is expected to push m³/d on `data.fluent` |
+| `temperature` | &deg;C | stored as supplied (Celsius); `_calcOxygenSaturation(T)` expects &deg;C |
+
+This is a known divergence from the platform-wide canonical-unit rule (`Pa` / `m³/s` / `W` / `K`). Tracked.
+
+---
+
+## Child registration
+
+Source: `src/specificClass.js` `configure()` (ChildRouter wiring) + `BaseReactorEngine._connectMeasurement` / `_connectReactor`.
+
+| Software type | Filter | Wired to | Side-effect |
+|:---|:---|:---|:---|
+| `measurement` | `asset.type = 'temperature'`, `positionVsParent = atEquipment` | `engine._connectMeasurement` &rarr; `_updateMeasurement` | Writes `engine.temperature`. CSTR only honours this. |
+| `measurement` | `asset.type = 'quantity (oxygen)'`, `positionVsParent = <numeric distance>` | `engine._connectMeasurement` &rarr; `Reactor_PFR._updateMeasurement` | **PFR only.** Maps measurement to nearest grid cell by `clamp(round(pos / length &times; n_x), 0, n_x &minus; 1)`. Writes into `state[cell][S_O_INDEX]`. |
+| `reactor` | `positionVsParent = 'upstream'` | `engine._connectReactor` | Subscribes to upstream reactor's `stateChange`. Each event triggers downstream `updateState`, which pulls upstream `getEffluent` into `Fs[0]` / `Cs_in[0]` before integrating. |
+
+### Not a child: `diffuser`
+
+`diffuser` (Equipment Module) is **not** registered as a reactor child. It feeds aeration via the `data.otr` topic on Port 0. No child-registration handshake is involved. If you want the diffuser's OTR to drive the reactor, wire the diffuser's process output to the reactor's input directly.
+
+### Unrecognised softwareType
+
+`BaseReactorEngine.registerChild` logs `Unrecognized softwareType: <x>` and drops the registration. There is no `valve`, `rotatingMachine`, etc. acceptance path.
+
+---
+
+## Related pages
+
+| Page | Why |
+|:---|:---|
+| [Home](Home) | Intuitive overview |
+| [Reference &mdash; Architecture](Reference-Architecture) | Code map, integration sequence, kinetics |
+| [Reference &mdash; Examples](Reference-Examples) | Shipped flows + debug recipes |
+| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
+| [EVOLV &mdash; Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions) | Platform-wide topic rules |
+| [EVOLV &mdash; Telemetry](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Telemetry) | Port 0 / 1 / 2 InfluxDB layout |

wiki/Reference-Examples.md

@@ -0,0 +1,160 @@
+# Reference — Examples
+
+![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
+
+> [!NOTE]
+> Every example flow shipped under `nodes/reactor/examples/`, plus how to load them, what they show, and the debug recipes that go with them. Live source: `nodes/reactor/examples/`.
+>
+> Pending full node review (2026-05). The current flows predate the standard 3-tier example-flow rework that `rotatingMachine` has completed; planned upgrade is tracked in the EVOLV superproject memory ("Example Flows" TODO).
+
+---
+
+## Shipped examples
+
+| File | Tier | Dependencies | What it shows |
+|:---|:---:|:---|:---|
+| `basic.flow.json` | 1 | EVOLV only | Single CSTR with one inlet. Inject `data.fluent` to set influent, `data.clock` to advance the integrator; watch `Fluent` effluent on Port 0 and InfluxDB scalars on Port 1. |
+| `integration.flow.json` | 2 | EVOLV only | Upstream `reactor` → `reactor` → `settler` chain. The downstream reactor registers the upstream via `child.register positionVsParent=upstream`; on each upstream `stateChange` the downstream pulls effluent and advances. |
+| `edge.flow.json` | 3 | EVOLV only | PFR with axial dispersion (`data.dispersion`) and multi-inlet (`n_inlets > 1`). Emits both `GridProfile` and `Fluent` per advance. |
+
+> [!IMPORTANT]
+> **Screenshots needed.** Editor capture of each example flow. Save as `wiki/_partial-screenshots/reactor/{01-basic-cstr,02-chain,03-pfr-edge}.png`. Replace these callouts with image links once captured.
+
+The legacy `additional_nodes/recirculation-pump` and `additional_nodes/settling-basin` Node-RED nodes are shipped from this repo but are not yet refactored to BaseDomain — they aren't part of these examples.
+
+---
+
+## Loading a flow
+
+### Via the editor
+
+1. Open the Node-RED editor at `http://localhost:1880`.
+2. Menu → Import → drag the JSON file.
+3. Click Deploy.
+
+### Via the Admin API
+
+```bash
+curl -X POST -H 'Content-Type: application/json' \
+  --data @nodes/reactor/examples/basic.flow.json \
+  http://localhost:1880/flows
+```
+
+---
+
+## Example — Basic CSTR
+
+Single-reactor flow with one inlet and the minimum set of inputs needed to drive nitrification.
+
+### What to do after deploy
+
+1. Inject `data.temperature` with `payload: 15` (or whatever process T you want). Optional — default is 20 °C.
+2. Inject `data.fluent` with:
+   ```json
+   {
+     "topic": "data.fluent",
+     "payload": {
+       "inlet": 0,
+       "F": 1000,
+       "C": [0, 30, 70, 25, 0, 0, 5, 1000, 100, 2000, 0, 200, 3500]
+     }
+   }
+   ```
+   Note `C[11] = 200` (X_A — autotroph biomass). If you copy the HTML default of `0.001`, nitrification never starts.
+3. If `kla > 0` is configured, you can skip OTR injection; the engine aerates internally. Otherwise inject `data.otr` with a positive scalar.
+4. Inject `data.clock` repeatedly (or rely on the periodic tick — `tickInterval = 1000` ms wall-clock). Each advance integrates `n_iter = floor(speedUpFactor · Δt / timeStep_days)` internal steps.
+5. Watch the debug tap on Port 0: `Fluent` envelopes with the 13-species effluent. `S_NH` should fall, `S_NO` should rise — nitrification is proceeding.
+
+> [!IMPORTANT]
+> **GIF needed.** Demo recording of `S_NH` ↓ / `S_NO` ↑ over 30 simulated days. Save as `wiki/_partial-gifs/reactor/01-basic-cstr.gif`.
+
+---
+
+## Example — Reactor chain
+
+Upstream → downstream coupling demo. The downstream reactor registers the upstream via:
+
+```json
+{
+  "topic": "child.register",
+  "payload": "<upstream-reactor-node-id>",
+  "positionVsParent": "upstream"
+}
+```
+
+On every upstream `stateChange`, `engine._connectReactor` triggers downstream `updateState`. That call first reads `upstream.getEffluent` into the downstream's `Fs[0]` / `Cs_in[0]`, then integrates. So one `data.clock` to the upstream advances the whole chain.
+
+> [!NOTE]
+> Pending full node review (2026-05). The flow currently in `integration.flow.json` may not yet conform to the multi-tab layout standard (Process Plant / Dashboard UI / Demo Drivers / Setup) described in `.claude/rules/node-red-flow-layout.md` &mdash; planned upgrade tracked in the EVOLV "Example Flows" TODO.
+
+---
+
+## Example &mdash; PFR edge
+
+Plug-flow reactor with axial discretization. After deploy:
+
+1. Inject `data.dispersion` with `payload: <m²/d>` to set the axial dispersion coefficient `D`.
+2. Inject one or more `data.fluent` messages with distinct `inlet` indices (0..`n_inlets &minus; 1`).
+3. Drive with `data.clock` as usual.
+4. Watch Port 0: each advance emits a `GridProfile` **before** the `Fluent`. The grid has `n_x` rows, 13 columns each.
+5. Add a `measurement` child with `asset.type = 'quantity (oxygen)'` and a numeric `positionVsParent` (e.g. `5` for 5 m from the inlet). On each measurement event the PFR engine writes the value into the nearest grid cell's `S_O`.
+
+Stability tips:
+
+- `Pe_local = d_x &middot; sum(Fs) / (D &middot; A)` must be `< 2` &mdash; if you see `Local Peclet number ... is too high!`, either increase `resolution_L` (more cells, smaller `d_x`) or raise `D`.
+- `Co_D = D &middot; timeStep / d_x²` must be `< 0.5` for the explicit FD scheme &mdash; if you see `Courant number ... is too high!`, decrease `timeStep`.
+
+---
+
+## Debug recipes
+
+| Symptom | First thing to check | Where to look |
+|:---|:---|:---|
+| `S_NH` stays at its initial value &mdash; nitrification not proceeding | `initialState.X_A` is effectively zero (HTML default is `0.001` mg/L). Set to `~50` or higher to seed autotrophs. | `reactor.html` &harr; `generalFunctions/src/configs/reactor.json` `initialState.X_A` |
+| `Fluent` payload `F = 0` | No `data.fluent` arrived, or `Fs[0]` is still 0 (no inlet flow). Check the message payload shape: `{inlet, F, C}`. | `src/commands/handlers.js` `dataFluent`, engine `setInfluent` |
+| `Fluent` payload appears, but `C` array is all zeros / unchanged | `data.clock` not arriving, or `n_iter = 0` (timestamp delta too small for the configured `timeStep`). Bump `speedUpFactor` or check that clock injects are firing. | `engine.updateState` in `baseEngine.js` |
+| PFR `GridProfile` not emitted | `reactor.reactor_type` is `CSTR` &mdash; only PFR has a grid profile. | `nodeClass._emitOutputs`, `pfr.getGridProfile` |
+| `temperature` ignored | Payload is non-numeric, or wrapped as `{value: ...}` with `value` non-finite. Look for `Invalid temperature input: <raw>` in the log. | `baseEngine.js` `setTemperature` setter |
+| Temperature child measurement not reconciling | The child's `asset.type` must be exactly `'temperature'` and `positionVsParent = atEquipment`. Anything else logs `Type '<x>' not recognized for measured update.` | `baseEngine.js` `_updateMeasurement` |
+| `Local Peclet number ... is too high!` warning on every PFR `updateState` | Either `D` is too small, or `d_x` is too large. Increase `resolution_L` or set a larger dispersion. | `pfr.updateState` Peclet guard |
+| `Courant number ... is too high!` warning | `timeStep` is too large for the configured `D`. Reduce it. | `pfr.updateState` Courant guard |
+| Settler downstream not updating | Settler must subscribe to the **reactor's `emitter`**, not `reactor.measurements.emitter`. Historical bug in `settler/src/specificClass.js` `_connectReactor` (fixed 2026-03-02). | upstream chain wiring, `settler._connectReactor` |
+| `wiki:datamodel` autogen script slow / timing out | `mathjs` cold-start is ~13 s. The current 60 s wrapper sometimes times out. | known limitation; fall back to the hand-curated Concrete sample in `CONTRACT.md` `Home.md` |
+| `reactor_type: 'pfr'` (lowercase) silently runs CSTR | Schema validator lowercases the enum; `_buildEngine` calls `.toUpperCase()` to compensate. If you stripped that guard, lowercase `pfr` falls through to the default branch (CSTR). | `src/specificClass.js` `_buildEngine` |
+| `data.otr` value ignored | `reactor.kla > 0`. The engine prefers internal `kla &middot; (sat &minus; S_O)` over external OTR. Set `kla = NaN` to enable external OTR. | `cstr.tick` / `pfr.tick` `klaIsNaN` branch |
+
+> Never ship `enableLog: 'debug'` in a demo &mdash; the kinetics engines log per-step on debug, which fills the container log within seconds.
+
+---
+
+## Docker compose snippet
+
+To bring up Node-RED + InfluxDB with EVOLV nodes pre-loaded:
+
+```yaml
+# docker-compose.yml (extract)
+services:
+  nodered:
+    build: ./docker/nodered
+    ports: ['1880:1880']
+    volumes:
+      - ./docker/nodered/data:/data/evolv
+  influxdb:
+    image: influxdb:2.7
+    ports: ['8086:8086']
+```
+
+Full file: [EVOLV/docker-compose.yml](https://gitea.wbd-rd.nl/RnD/EVOLV/src/branch/development/docker-compose.yml).
+
+---
+
+## Related pages
+
+| Page | Why |
+|:---|:---|
+| [Home](Home) | Intuitive overview |
+| [Reference &mdash; Contracts](Reference-Contracts) | Topic + config + child filters |
+| [Reference &mdash; Architecture](Reference-Architecture) | Code map, kinetics engines, integration sequence |
+| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
+| [settler &mdash; Examples](https://gitea.wbd-rd.nl/RnD/settler/wiki/Reference-Examples) | The typical downstream Unit |
+| [EVOLV &mdash; Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns) | Where reactor fits in a larger plant |

wiki/Reference-Limitations.md

@@ -0,0 +1,132 @@
+# Reference — Limitations
+
+![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
+
+> [!NOTE]
+> What `reactor` does not do, current rough edges, and open questions. Open items live in `.agents/improvements/IMPROVEMENTS_BACKLOG.md` and `.claude/refactor/OPEN_QUESTIONS.md` in the superproject.
+>
+> Pending full node review (2026-05). Content reflects `CONTRACT.md`, the current source, and a partial walkthrough of `src/kinetics/` — not a full audit.
+
+---
+
+## When you would not use this node
+
+| Scenario | Use instead |
+|:---|:---|
+| A passive equalisation tank (no biological reactions, just buffering) | A simple Node-RED buffer / function node — the kinetics engines assume reactions are happening. |
+| A residence-time delay (plug-flow without ASM) | A delay node or custom buffer; the ASM3 13-species machinery + `mathjs` cold-start are overkill. |
+| Aerobic-only contactors where you only need oxygen mass-transfer | An OTR-only model is lighter; ASM3 brings 13 species you'll ignore. |
+| A clarifier / settler | `settler` — reactor has no settling, no sludge thickening, no underflow / overflow split. |
+| A pump / blower / valve | `rotatingMachine` / `valve` — reactor is a process-tank model, not an actuator. |
+| Anaerobic digestion | ASM3 is calibrated for activated sludge under aerobic / anoxic conditions. ADM1 (a separate model family) is the right tool for digesters. |
+
+---
+
+## Known limitations
+
+### `X_A` initial default footgun
+
+The HTML editor form's default for initial autotroph biomass is **`0.001` mg/L** (effectively zero). The JSON schema default is `200` mg/L. The HTML wins at deploy time. With `X_A ≈ 0` nitrification never starts — `S_NH` stays at the influent value forever, no `S_NO` is produced.
+
+> [!WARNING]
+> Always open every deployed reactor node and confirm `Initial X_A` is `≥ ~50` mg/L before expecting nitrification. Tracked in `CONTRACT.md` `## 14` row 2 and in EVOLV memory `MEMORY.md` "Key Integration Gotchas".
+
+### `mathjs` cold-start ~13 s
+
+`baseEngine.js` requires `mathjs`. The first `require('mathjs')` in a Node.js process takes ~13 s wall-clock to initialise. This delays first `data.clock` advance after a fresh deploy, and can time out the `wiki:datamodel` autogen wrapper (60 s budget). Two remedies tracked:
+
+1. Tree-shake `mathjs` to only the operations actually used (`add`, `multiply`, `diag`, `resize`, `sum`, `divide`).
+2. Lazy-initialise / cache the instance.
+
+Tracked in `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load".
+
+### `timeStep` unit mismatch
+
+- HTML form label: `Time step [s]`.
+- Schema (`generalFunctions/src/configs/reactor.json` line ~144): `unit: "h"`.
+- `baseEngine.js` line ~40 converts by `÷ 86400` (seconds → days) before using it.
+
+The conversion suggests the **true** unit is seconds. Schema is wrong. Until reconciled, treat the form field as seconds. Tracked in `CONTRACT.md` `## 14` row 7 and in `OPEN_QUESTIONS.md` (Phase 5/6 cleanup list).
+
+### `reactor_type` enum casing
+
+The JSON schema validator lowercases `reactor_type` (so `'PFR'` → `'pfr'`). `Reactor._buildEngine` calls `.toUpperCase()` to compensate. If that guard is ever removed prematurely (before the platform-wide canonical casing rule is decided in Phase 7), PFR configs silently fall back to the default branch — which constructs a CSTR. Tracked in `OPEN_QUESTIONS.md`.
+
+### `getEffluent` shape historically varied
+
+Earlier versions of `BaseReactorEngine.getEffluent` returned either an envelope object or an array of envelopes (multi-outlet PFR). The current code emits a single `{topic, payload, timestamp}` envelope, but the downstream `settler._connectReactor` tolerates **both** shapes. Don't break this contract without coordinating with the settler node. EVOLV memory records a 2026-03-02 fix in settler for the array-vs-envelope assumption.
+
+### No FSM — no mode / setpoint / startup-shutdown sequencing
+
+reactor has no startup, no shutdown, no e-stop, no mode, no setpoint. It runs continuous-state ODE / PDE integration unconditionally as long as `data.clock` advances (or the tick loop fires). A downstream consumer that expects a `state` field on Port 0 will get nothing of the sort. This is by design — biological reactors don't have meaningful FSM states — but it's a divergence from `rotatingMachine` / `pumpingStation` patterns that callers should know about.
+
+### No mode / source / action allow-list gating
+
+All incoming topics are accepted as long as the payload validates. There is no `parent` / `GUI` / `fysical` source-gating, no `auto` / `virtualControl` / `fysicalControl` mode-gating. If you want to lock down a deployed reactor (e.g. ignore manual `data.fluent` injections while a real flow sensor is wired), you must do it externally.
+
+### `additional_nodes/` legacy companions not refactored
+
+`additional_nodes/recirculation-pump.js` and `additional_nodes/settling-basin.js` are sibling Node-RED nodes shipped from the reactor repo (because they share the same package context). They are **not yet refactored to BaseDomain**. Tracked as P6.5 follow-up.
+
+### `reaction_modules/` legacy directory
+
+`src/reaction_modules/asm3_class.js` is consumed by the current engines. `src/reaction_modules/asm3_class Koch.js` is a legacy plug-in variant **not consumed by anything in the current codebase**. Removal pending. Tracked as P6.5 follow-up.
+
+### Units don't follow EVOLV canonical-unit rule
+
+The platform-wide MeasurementContainer canonical units are `Pa` / `m³/s` / `W` / `K`. reactor uses m³/d for flow, °C for temperature, mg/L (or mmol/L for alkalinity) for concentrations. No conversion at the system boundary. Calling code that expects canonical units must convert.
+
+### `data.dispersion` is silently a no-op on CSTR
+
+`specificClass.set setDispersion` checks `if (this.engine instanceof Reactor_PFR)` before forwarding. On a CSTR the setter just drops the payload — no warn, no error. If you deploy a flow that injects `data.dispersion` and switch the reactor type to CSTR, the injection is silently ignored.
+
+### Single output-shape convention not documented per-key
+
+The `getOutput()` implementation **omits** non-finite species values (`Number.isFinite` guard) rather than emitting them as `null`. Per `.claude/rules/output-coverage.md`, every node should pick one convention and document it. reactor's is "absent" — downstream consumers should treat a missing species key as "not produced this tick", never as zero.
+
+### `output-coverage` manifest not yet present
+
+`test/_output-manifest.md` (required by the platform-wide output-coverage rule, 2026-05-14) is not yet checked in for reactor. The Port-0 envelope shape, Port-1 InfluxDB fields, and `GridProfile` payload all need enumeration with populated + degraded test coverage. Tracked in `.agents/improvements/IMPROVEMENTS_BACKLOG.md`.
+
+---
+
+## Open questions (tracked)
+
+| Question | Where it lives |
+|:---|:---|
+| `mathjs` slow load — tree-shake or lazy-init | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" |
+| `reactor_type` enum casing — platform-wide canonical | `.claude/refactor/OPEN_QUESTIONS.md` — "reactor schema enum lowercases reactor_type" |
+| `timeStep` unit reconciliation (HTML `s` vs schema `h` vs engine `d`) | `OPEN_QUESTIONS.md` Phase 5/6 cleanup list |
+| Removal of `reaction_modules/asm3_class Koch.js` and `additional_nodes/*` | P6.5 follow-up |
+| Output-coverage manifest + populated / degraded tests | `.agents/improvements/IMPROVEMENTS_BACKLOG.md` |
+| Should reactor adopt a canonical-unit boundary like the rest of EVOLV? | Internal — not yet ticketed |
+| Multi-outlet PFR (separate effluent streams per spatial point) | Internal — long-term |
+
+---
+
+## Migration notes
+
+### From the pre-`BaseDomain` reactor
+
+The current `specificClass` extends `BaseDomain` and uses ChildRouter to dispatch `measurement` / `reactor` registrations. Older flows that pre-date this refactor may have hand-wired child handlers; redeploying after `npm install` should pick up the new path automatically — no schema migration is required.
+
+### From legacy topic names
+
+The five `data.*` topics replace the pre-canonical PascalCase aliases (`Fluent`, `OTR`, `Temperature`, `Dispersion`, `clock`). The aliases are still accepted and emit a one-time deprecation warning on first use, but will be removed in Phase 7. Migrate flows by renaming the topic string on each inject.
+
+### From hand-counted internal steps
+
+Before the `speedUpFactor` field, simulation acceleration required adjusting `timeStep`. The current path is to leave `timeStep` at its physically-meaningful value (~1 s) and crank `speedUpFactor` to advance more process-time per wall-clock second. Old flows with abnormally large `timeStep` should be re-saved with the new field.
+
+---
+
+## Related pages
+
+| Page | Why |
+|:---|:---|
+| [Home](Home) | Intuitive overview |
+| [Reference — Contracts](Reference-Contracts) | Topic + config + child filters |
+| [Reference — Architecture](Reference-Architecture) | Code map, kinetics engines, integration sequence |
+| [Reference — Examples](Reference-Examples) | Shipped flows + debug recipes |
+| [settler — Limitations](https://gitea.wbd-rd.nl/RnD/settler/wiki/Reference-Limitations) | The downstream Unit's quirks (incl. the historical `getEffluent` shape tolerance) |
+| [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home) | The Equipment node that pushes `data.otr` — not a registered child |

wiki/_Sidebar.md

@@ -0,0 +1,20 @@
+### reactor
+
+- [Home](Home)
+
+**Reference**
+
+- [Contracts](Reference-Contracts)
+- [Architecture](Reference-Architecture)
+- [Examples](Reference-Examples)
+- [Limitations](Reference-Limitations)
+
+**Related**
+
+- [EVOLV master wiki](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Home)
+- [settler wiki](https://gitea.wbd-rd.nl/RnD/settler/wiki/Home)
+- [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home)
+- [measurement wiki](https://gitea.wbd-rd.nl/RnD/measurement/wiki/Home)
+- [Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns)
+- [Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions)
+- [Telemetry](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Telemetry)