docs(wiki): rewrite Home.md to full 14-section visual-first template

- 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 <noreply@anthropic.com>

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 If this banner is stale, the page may be out of date.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<br/>upstream<br/>Unit]:::unit
     reactor[reactor<br/>Unit]:::unit
     settler[settler<br/>downstream<br/>Unit]:::unit
-    pump[rotatingMachine<br/>downstream<br/>Equipment]:::equip
+    diffuser[diffuser<br/>Equipment]:::equip
     tsens[measurement<br/>temperature<br/>atequipment]:::ctrl
-    osens[measurement<br/>oxygen<br/>position]:::ctrl
+    osens[measurement<br/>oxygen<br/>at distance]:::ctrl
 
     upstream -.stateChange.-> reactor
     reactor -->|Fluent inlet=0| settler
-    pump -->|child.register downstream| reactor
+    settler -.stateChange.-> reactor
-    tsens -->|temperature.measured.atequipment| reactor
+    diffuser -->|data.otr| reactor
-    osens -->|quantity (oxygen).measured.&lt;position&gt;| 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.<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. |
@@ -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()<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"]
+        sc["Reactor.configure()<br/>_flattenEngineConfig()<br/>_buildEngine() → CSTR or PFR<br/>ChildRouter.onRegister rules"]
     end
     subgraph kinetics["src/kinetics/"]
-        be["baseEngine.js<br/>shared ASM3 rate vector"]
+        be["baseEngine.js<br/>BaseReactorEngine<br/>influent state, OTR, T<br/>_connectMeasurement / _connectReactor<br/>updateState() → n_iter ticks"]
-        cstr["cstr.js<br/>0-D integrator"]
+        cstr["cstr.js<br/>Reactor_CSTR extends BaseReactorEngine<br/>Forward-Euler 0-D integrator"]
-        pfr["pfr.js<br/>spatial discretization + dispersion"]
+        pfr["pfr.js<br/>Reactor_PFR extends BaseReactorEngine<br/>FD spatial grid + Danckwerts BC"]
     end
     subgraph commands["src/commands/"]
-        cmds["index.js + handlers.js<br/>6 input topics"]
+        cmds["index.js — 6 descriptors<br/>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<br/>temperature"]:::ctrl
+        m_t["measurement<br/>temperature<br/>positionVsParent=atEquipment"]:::ctrl
-        m_o["measurement<br/>quantity (oxygen)"]:::ctrl
+        m_o["measurement<br/>quantity (oxygen)<br/>positionVsParent=distance (numeric)"]:::ctrl
-        r_up["reactor<br/>upstream"]:::unit
+        r_up["reactor<br/>positionVsParent=upstream"]:::unit
     end
-    m_t -->|temperature.measured.atEquipment| h_meas[engine._connectMeasurement]
+    m_t -->|temperature.measured.atEquipment| h_meas["engine._connectMeasurement<br/>(baseEngine.js)"]
-    m_o -->|quantity (oxygen).measured.&lt;pos&gt;| h_meas
+    m_o -->|quantity(oxygen).measured.distance| h_meas
-    r_up -.stateChange.-> h_react[engine._connectReactor]
+    r_up -.stateChange.-> h_react["engine._connectReactor<br/>(baseEngine.js)"]
-    h_meas --> reconcile[reconcile T / O2 into engine state]
+    h_meas --> reconcile["reconcile T → engine.temperature<br/>reconcile O2 → state grid cell (PFR only)"]
-    h_react --> pull[pull upstream effluent → Fs/Cs_in]
+    h_react --> pull["pull upstream getEffluent<br/>→ 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.<distance>` → nearest grid cell DO. |
+| `measurement` | `asset.type = temperature`, `positionVsParent = atEquipment` | `engine._connectMeasurement` | Writes `engine.temperature`. CSTR only honours temperature; PFR additionally reconciles `quantity (oxygen).measured.<distance>` (numeric position) → 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 = quantity (oxygen)`, `positionVsParent = <numeric distance>` | `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 reactor as reactor (specificClass)
-    participant engine as kinetics engine
+    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,<br/>each timeStep × speedUpFactor
+    Note over engine: n_iter = floor(speedUpFactor × Δt / timeStep)<br/>each step calls tick(timeStep)
-    engine->>engine: integrate ASM3 rates
+    engine->>engine: integrate ASM3 rates (CSTR: Forward Euler / PFR: FD)
-    engine->>engine: emit 'stateChange'
+    engine->>engine: cap S_O to saturation, clip negatives to 0
-    reactor->>reactor: notifyOutputChanged
+    engine->>engine: emit 'stateChange' (currentTime)
-    reactor->>out: Fluent { inlet=0, F, C[13] }
+    reactor->>reactor: notifyOutputChanged → getOutput()
-    alt PFR
+    reactor->>out: getOutput() → {flow_total, temperature, S_O … X_TS}
-        reactor->>out: GridProfile { grid, n_x, d_x, … }
+    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"]
+    subgraph editor["Node-RED editor form (reactor.html)"]
-        f1[Reactor type CSTR / PFR]
+        f1["Reactor type: CSTR / PFR"]
-        f2[Volume m3]
+        f2["Volume (m³)"]
-        f3[Length m + resolution]
+        f3["Length (m) + Resolution — PFR only"]
-        f4[Alpha dispersion]
+        f4["Alpha α (boundary condition blend)"]
-        f5[KLa 1/h]
+        f5["Number of inlets"]
-        f6[Time step + speed-up]
+        f6["kLa (d⁻¹) — internal aeration"]
-        f7[Initial state 13 species]
+        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<br/>reactor.resolution_L]
+        c3["reactor.length<br/>reactor.resolution_L"]
         c4[reactor.alpha]
-        c5[reactor.kla]
+        c5[reactor.n_inlets]
-        c6[reactor.timeStep<br/>reactor.speedUpFactor]
+        c6[reactor.kla]
-        c7[initialState.* ASM3 keys]
+        c7["initialState.S_O … X_TS"]
+        c8["reactor.timeStep (unit: h per schema)<br/>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 |
+| Resolution | `reactor.resolution_L` | `10` | ≥ 1 | PFR grid cell count `n_x` |
-| Alpha | `reactor.alpha` | `0.5` | 0–1 | dispersion vs plug-flow blend |
+| 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`) |
+| kLa (d⁻¹) | `reactor.kla` | `0` | ≥ 0; set to `NaN` to use `data.otr` instead | `_calcOTR()` in `baseEngine.js` |
-| Time step (h) | `reactor.timeStep` | `0.001` | ≥ 0.0001 | integrator inner step |
+| 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 | wall-clock → process-time multiplier |
+| 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" |
+| 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` 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` |
+| 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 |