reactor/wiki/Home.md

# reactor

> **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 If this banner is stale, the page may be out of date.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

**reactor** is an S88 Unit that wraps an ASM3 biological-process engine — either a CSTR (fully mixed tank) or a PFR (plug-flow with axial dispersion). It integrates 13 species (S_O, S_NH, X_H, X_TS, …) and emits the effluent vector each tick. Drives a settler downstream and accepts a recirculation pump child.

## 2. Position in the platform

~~~mermaid
flowchart LR
    upstream[reactor<br/>upstream<br/>Unit]:::unit
    reactor[reactor<br/>Unit]:::unit
    settler[settler<br/>downstream<br/>Unit]:::unit
    diffuser[diffuser<br/>Equipment]:::equip
    tsens[measurement<br/>temperature<br/>atequipment]:::ctrl
    osens[measurement<br/>oxygen<br/>at distance]:::ctrl

    upstream -.stateChange.-> reactor
    reactor -->|Fluent inlet=0| settler
    settler -.stateChange.-> reactor
    diffuser -->|data.otr| reactor
    tsens -->|child.register| reactor
    osens -->|child.register| reactor
    tsens -->|temperature.measured.atEquipment| reactor
    osens -->|quantity(oxygen).measured.distance| reactor
    classDef unit fill:#50a8d9,color:#000
    classDef equip fill:#86bbdd,color:#000
    classDef ctrl fill:#a9daee,color:#000
~~~

S88 colours: Unit `#50a8d9`, Equipment `#86bbdd`, Control Module `#a9daee`. Source of truth: `.claude/rules/node-red-flow-layout.md`.

reactor sits at the Unit level. A diffuser (Equipment) sends aeration rates via `data.otr` — it is NOT registered as a child. Measurement children (Control Module) register and supply temperature or dissolved-oxygen reconciliation. Settler is a downstream Unit that listens to `stateChange` to pull effluent; an upstream reactor drives this reactor the same way.

## 3. Capability matrix

| Capability | Status | Notes |
|---|---|---|
| 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`. 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. |
| Dispersion override (PFR) | ✅ | `data.dispersion` updates axial `D`. |
| Hot-swap engine type | ❌ | `reactor_type` is read once in `configure()`. |

## 4. Code map

~~~mermaid
flowchart TB
    subgraph nodeRED["nodeClass.js — adapter (BaseNodeAdapter)"]
        nc["buildDomainConfig()<br/>static DomainClass = Reactor<br/>static commands"]
    end
    subgraph domain["specificClass.js — orchestrator (BaseDomain)"]
        sc["Reactor.configure()<br/>_flattenEngineConfig()<br/>_buildEngine() → CSTR or PFR<br/>ChildRouter.onRegister rules"]
    end
    subgraph kinetics["src/kinetics/"]
        be["baseEngine.js<br/>BaseReactorEngine<br/>influent state, OTR, T<br/>_connectMeasurement / _connectReactor<br/>updateState() → n_iter ticks"]
        cstr["cstr.js<br/>Reactor_CSTR extends BaseReactorEngine<br/>Forward-Euler 0-D integrator"]
        pfr["pfr.js<br/>Reactor_PFR extends BaseReactorEngine<br/>FD spatial grid + Danckwerts BC"]
    end
    subgraph commands["src/commands/"]
        cmds["index.js — 6 descriptors<br/>handlers.js — 6 pure fns"]
    end
    nc --> sc
    nc --> cmds
    sc --> be
    cstr --> be
    pfr --> be
~~~

| Module | Owns | Read first if you're changing… |
|---|---|---|
| `kinetics/baseEngine.js` | ASM3 stoichiometry + rate vector + species list. | Stoichiometric matrix, kinetic constants. |
| `kinetics/cstr.js` | 0-D CSTR integrator + `_connectMeasurement` + `_connectReactor`. | Mixed-tank behaviour, child wiring. |
| `kinetics/pfr.js` | Axial discretization, dispersion, grid profile emission. | PFR-specific behaviour, grid math. |
| `commands/` | 6 input descriptors + handlers (clock, fluent, OTR, temperature, dispersion, child). | Inbound topic API, alias deprecation. |
| `reaction_modules/` | Optional plug-in reaction modules (legacy — not yet refactored). | Adding new bio-process modules. |
| `additional_nodes/` | Sibling Node-RED nodes (`recirculation-pump`, `settling-basin`) shipped from this repo. | Cross-node deploy in same package. |

## 5. Topic contract

> **Auto-generated** from `src/commands/index.js`. Do NOT hand-edit between the markers. Re-run `npm run wiki:contract`.

<!-- 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 -->

## 6. Child registration

~~~mermaid
flowchart LR
    subgraph kids["accepted children (softwareType)"]
        m_t["measurement<br/>temperature<br/>positionVsParent=atEquipment"]:::ctrl
        m_o["measurement<br/>quantity (oxygen)<br/>positionVsParent=distance (numeric)"]:::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.distance| h_meas
    r_up -.stateChange.-> h_react["engine._connectReactor<br/>(baseEngine.js)"]
    h_meas --> reconcile["reconcile T → engine.temperature<br/>reconcile O2 → state grid cell (PFR only)"]
    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` | `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. |
| `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
sequenceDiagram
    participant clock as clock injector
    participant reactor as reactor (specificClass)
    participant engine as kinetics engine (CSTR/PFR)
    participant downstream as settler / next reactor
    participant out as Port-0 output

    clock->>reactor: data.clock { timestamp }
    reactor->>engine: updateState(timestamp)
    Note over engine: n_iter = floor(speedUpFactor × Δt / timeStep)<br/>each step calls tick(timeStep)
    engine->>engine: integrate ASM3 rates (CSTR: Forward Euler / PFR: FD)
    engine->>engine: cap S_O to saturation, clip negatives to 0
    engine->>engine: emit 'stateChange' (currentTime)
    reactor->>reactor: notifyOutputChanged → getOutput()
    reactor->>out: getOutput() → {flow_total, temperature, S_O … X_TS}
    alt PFR engine
        reactor->>out: GridProfile { grid[n_x][13], n_x, d_x, length, species }
    end
    out->>downstream: Fluent { inlet=0, F, C[13] } via stateChange listener
~~~

`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()`

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):

```json
{
  "flow_total": 1000,
  "temperature": 15.2,
  "S_O": 2.1,
  "S_I": 30,
  "S_S": 12.4,
  "S_NH": 0.8,
  "S_N2": 4.3,
  "S_NO": 18.6,
  "S_HCO": 4.2,
  "X_I": 1050,
  "X_S": 65,
  "X_H": 2150,
  "X_STO": 4.5,
  "X_A": 215,
  "X_TS": 3680
}
```

Species ordering follows ASM3: indices 0–6 are soluble, 7–12 are particulate. `flow_total` is the effluent flow (m³/d); the reactor uses days as the time unit internally.

## 9. Configuration — editor form ↔ config keys

~~~mermaid
flowchart TB
    subgraph editor["Node-RED editor form (reactor.html)"]
        f1["Reactor type: CSTR / PFR"]
        f2["Volume (m³)"]
        f3["Length (m) + Resolution — PFR only"]
        f4["Alpha α (boundary condition blend)"]
        f5["Number of inlets"]
        f6["kLa (d⁻¹) — internal aeration"]
        f7["13 × initial concentration fields"]
        f8["Time step (s label) + Speed-up factor"]
    end
    subgraph config["Domain config slice (reactor.json)"]
        c1[reactor.reactor_type]
        c2[reactor.volume]
        c3["reactor.length<br/>reactor.resolution_L"]
        c4[reactor.alpha]
        c5[reactor.n_inlets]
        c6[reactor.kla]
        c7["initialState.S_O … X_TS"]
        c8["reactor.timeStep (unit: h per schema)<br/>reactor.speedUpFactor"]
    end
    f1 --> c1
    f2 --> c2
    f3 --> c3
    f4 --> c4
    f5 --> c5
    f6 --> c6
    f7 --> c7
    f8 --> c8
~~~

| Form field | Config key | Schema default | Range | Where used |
|---|---|---|---|---|
| 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 | `reactor.resolution_L` | `10` | ≥ 1 | PFR grid cell count `n_x` |
| Alpha | `reactor.alpha` | `0.5` | 0–1 | Danckwerts (0) vs Dirichlet (1) inlet BC |
| Inlets | `reactor.n_inlets` | `1` | ≥ 1 | `Fs[]` / `Cs_in[]` array sizes |
| kLa (d⁻¹) | `reactor.kla` | `0` | ≥ 0; set to `NaN` to use `data.otr` instead | `_calcOTR()` in `baseEngine.js` |
| Time step | `reactor.timeStep` | `0.001` | ≥ 0.0001 | integrator inner step (schema says `h`; HTML label says `s` — see limitation #6) |
| Speed-up factor | `reactor.speedUpFactor` | `1` | ≥ 1 | `n_iter = floor(speedUpFactor × Δt_wall / timeStep_days)` |
| Initial S_O | `initialState.S_O` | `0` | ≥ 0 (mg/L) | starting dissolved oxygen (caps to saturation in first tick) |
| Initial S_NH | `initialState.S_NH` | `25` | ≥ 0 (mg/L) | starting ammonium |
| Initial X_H | `initialState.X_H` | `2000` | ≥ 0 (mg/L) | starting heterotroph biomass |
| Initial X_A | `initialState.X_A` | `200` | ≥ 0 (mg/L) | starting autotroph biomass — must be ≥ ~50 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

Skipped — reactor has no FSM. It runs continuous-state ODE integration; the engine's only stateful event is `stateChange`, fired after every successful integration advance. See section 7 for the integration sequence.

## 11. Examples

| Tier | File | What it shows | Status |
|---|---|---|---|
| Basic | `examples/basic.flow.json` | CSTR with one inlet, watch `Fluent` effluent | ✅ in repo |
| Integration | `examples/integration.flow.json` | upstream reactor → reactor → settler chain | ✅ in repo |
| Edge | `examples/edge.flow.json` | PFR with dispersion + multi-inlet | ✅ in repo |
| Companions | `additional_nodes/*` | recirculation-pump + settling-basin Node-RED nodes shipped from this repo | ✅ in repo |

One screenshot per tier where helpful. PNG ≤ 200 KB under `wiki/_partial-screenshots/reactor/`.

## 12. Debug recipes

| Symptom | First thing to check | Where to look |
|---|---|---|
| Nitrification doesn't proceed (S_NH stays high) | `initialState.X_A` must be ≥ ~50 mg/L. Defaulting to `0.001` (a known footgun) means no autotrophs. | `generalFunctions/src/configs/reactor.json` |
| `Fluent` effluent flow zero | No `data.clock` ticks arriving, or `data.fluent` never set `Fs[0] > 0`. | `commands/handlers.js`, engine `setInfluent` |
| PFR `GridProfile` not emitted | `reactor_type` set to `CSTR` — only PFR emits grid. | `_buildEngine` switch |
| Settler downstream not updating | `stateChange` event listener path: settler must subscribe to `reactor.emitter`, NOT `reactor.measurements.emitter`. | settler `_connectReactor` |
| Temperature reconcile silently ignored | Child measurement's `asset.type` not `temperature` exactly, or `positionVsParent` not `atEquipment`. | `engine._connectMeasurement` |
| Integrator slow / stalls | `reactor.timeStep` too small for `speedUpFactor`. Internal `n_iter` count blows up. | `engine.updateState` |
| `wiki:datamodel` script slow / hangs | `mathjs` cold-start ~13 s; instantiation depends on it transitively. See known-limitations row 1. | `kinetics/baseEngine.js` |

## 13. When you would NOT use this node

- Use reactor for **ASM3 biological treatment** modelling (activated sludge, nitrification, denitrification). For aerobic-only or simpler kinetics, the ASM3 species vector is overkill.
- Don't use reactor for a passive equalisation tank — the kinetics engines assume reactions are happening.
- Skip reactor when you only need a residence-time delay; a simple buffer node is lighter and doesn't require `mathjs`.

## 14. Known limitations / current issues

| # | Issue | Tracked in |
|---|---|---|
| 1 | `mathjs` cold-start adds ~13 s to first `require()` — `wiki:datamodel` auto-gen may time out on the 60 s wrapper. Falls back to the hand-curated `concrete sample` block. Two remedies tracked: tree-shake mathjs to used ops only; cache the instance. | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" |
| 2 | `initialState.X_A` HTML default is `0.001` mg/L (silently disabling nitrification) but the schema default is `200` mg/L. Always check the deployed node's form value before expecting nitrification. | `reactor.html` line 38 vs `generalFunctions/src/configs/reactor.json` |
| 3 | `getEffluent` shape historically varied (array vs single envelope) — settler's `_connectReactor` tolerates both. Don't break the contract without updating settler. | `nodes/settler/src/specificClass.js → _connectReactor` |
| 4 | `additional_nodes/recirculation-pump` and `settling-basin` are legacy companions — not yet refactored to BaseDomain. | P6.5 follow-up |
| 5 | `reaction_modules/` is a legacy plug-in directory not consumed by the current engines. Removal pending. | P6.5 follow-up |
| 6 | `reactor_type` enum casing: the JSON schema validator lowercases the user-supplied value (`'PFR'` → `'pfr'`). `Reactor._buildEngine` calls `.toUpperCase()` to work around this until Phase 7 decides the platform-wide canonical casing. If the guard is removed prematurely, PFR config silently falls back to CSTR. | `.claude/refactor/OPEN_QUESTIONS.md` — "reactor schema enum lowercases reactor_type" |
| 7 | `timeStep` unit mismatch: the HTML form label says "Time step [s]" but `reactor.json` declares `unit: "h"`. `baseEngine.js` converts `config.timeStep` by `÷ 86 400` (seconds → days), suggesting the true input unit is seconds. Audited in OPEN_QUESTIONS.md Phase 5/6 cleanup list. | `baseEngine.js` line 40; `reactor.json` `timeStep.rules.unit`; `reactor.html` time-step label |