fix: expose tick(dt) on Reactor wrapper

P6.5 refactor introduced the BaseDomain wrapper around CSTR/PFR engines
but didn't pass tick() through. BaseNodeAdapter's optional-chain
source.tick?.() got undefined and the kinetics engine never integrated
when driven through the new adapter (only via the explicit
_emitOutputs override that calls updateState).

Added tick(timeStep) that delegates to engine.tick + emits
'output-changed'. Tests that construct the wrapper (not the engine
directly) now work.

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

CONTRACT.md

@@ -0,0 +1,51 @@
+# reactor — Contract
+
+Hand-maintained for Phase 6; the `## Inputs` table is generated from
+`src/commands/index.js` (see Phase 9 generator). Keep ≤ 80 lines.
+
+## Inputs (msg.topic on Port 0)
+
+| Canonical | Aliases (deprecated) | Payload | Effect |
+|---|---|---|---|
+| `data.clock` | `clock` | `msg.timestamp` (ms since epoch) | Calls `source.updateState(timestamp)` — advances the ASM kinetics integrator by `n_iter` time steps that fit between `currentTime` and the supplied timestamp (scaled by `speedUpFactor`). |
+| `data.fluent` | `Fluent` | `{ inlet: number, F: number, C: number[13] }` | Writes the per-inlet flow rate (`F`, m³/d) and concentration vector (`C`) into `engine.Fs[inlet]` / `engine.Cs_in[inlet]`. |
+| `data.otr` | `OTR` | numeric | Sets the externally-supplied oxygen transfer rate (used when `kla` is NaN). |
+| `data.temperature` | `Temperature` | numeric or `{ value: number }` | Sets `engine.temperature` (°C). Non-numeric payloads are warned and ignored. |
+| `data.dispersion` | `Dispersion` | numeric | PFR only — sets the axial dispersion coefficient `D` (m²/d). |
+| `child.register` | `registerChild` | child node id (string) | Looks up the sibling node via `RED.nodes.getNode(id)` and delegates to `source.childRegistrationUtils.registerChild` with `msg.positionVsParent`. |
+
+Aliases log a one-time deprecation warning the first time they fire.
+
+## Outputs (msg.topic on Port 0/1/2)
+
+- **Port 0 (process):** every tick emits the engine's effluent:
+  `{ topic: 'Fluent', payload: { inlet: 0, F, C: number[13] }, timestamp }`.
+  For a PFR an additional `{ topic: 'GridProfile', payload: { grid, n_x, d_x, length, species, timestamp } }`
+  message goes out on the same port before the effluent.
+- **Port 1 (InfluxDB telemetry):** formatted via `outputUtils.formatMsg(..., 'influxdb')`
+  from `getOutput()` — carries `flow_total`, `temperature`, and one field per ASM3
+  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`).
+- **Port 2 (registration):** at startup the node sends one
+  `{ topic: 'child.register', payload: <node.id>, positionVsParent, distance }`
+  to its parent.
+
+## Events emitted by `source.emitter`
+
+- `stateChange` — fires after every `updateState()` that advances the integrator.
+  Payload is the new `currentTime` (ms since epoch). Downstream reactors register
+  via `child.register` and subscribe to this event to pull the upstream
+  effluent on each advance.
+- `output-changed` — base notification fired by `updateState()` so the
+  BaseNodeAdapter pipeline pushes outputs (currently used only as a heartbeat;
+  effluent is emitted directly from the periodic tick).
+
+## Children accepted
+
+- `measurement` — subscribes to `<type>.measured.<position>` on the child's
+  `measurements.emitter`. Recognised reconciliations: `temperature.measured.atEquipment`
+  writes `engine.temperature`; PFR additionally honours
+  `quantity (oxygen).measured.<distance>` to reconcile dissolved-oxygen
+  concentration into the nearest grid cell.
+- `reactor` — registers as the upstream reactor; the downstream `updateState`
+  pulls the upstream effluent into `Fs[0]` / `Cs_in[0]` before integrating.

package.json

@@ -17,7 +17,10 @@
   "author": "P.R. van der Wilt",
   "main": "reactor.js",
   "scripts": {
-    "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js"
+    "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js",
+    "wiki:contract":  "node ../generalFunctions/scripts/wikiGen.js contract  ./src/commands/index.js   --write ./wiki/Home.md",
+    "wiki:datamodel": "node ../generalFunctions/scripts/wikiGen.js datamodel ./src/specificClass.js     --write ./wiki/Home.md",
+    "wiki:all":       "npm run wiki:contract && npm run wiki:datamodel"
   },
   "node-red": {
     "nodes": {

src/commands/handlers.js

@@ -0,0 +1,25 @@
+'use strict';
+
+// Reactor input handlers. Each receives (source, msg, ctx) where source is
+// the Reactor domain and ctx is { node, RED, send, logger }. The handlers
+// either forward to engine setters or drive a synchronous state update.
+
+exports.dataClock = (source, msg) => {
+  source.updateState(msg.timestamp ?? Date.now());
+};
+
+exports.dataFluent     = (source, msg) => { source.setInfluent    = msg; };
+exports.dataOTR        = (source, msg) => { source.setOTR         = msg; };
+exports.dataTemperature = (source, msg) => { source.setTemperature = msg; };
+exports.dataDispersion = (source, msg) => { source.setDispersion  = msg; };
+
+exports.childRegister = (source, msg, ctx) => {
+  const childId = msg.payload;
+  const RED = ctx?.RED;
+  const childObj = RED?.nodes?.getNode?.(childId);
+  if (!childObj || !childObj.source) {
+    source?.logger?.warn?.(`registerChild skipped: missing child/source for id=${childId}`);
+    return;
+  }
+  source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
+};

src/commands/index.js

@@ -0,0 +1,47 @@
+'use strict';
+
+// reactor command registry. Canonical names follow CONTRACTS.md §1.
+// Legacy names (clock, Fluent, OTR, Temperature, Dispersion, registerChild)
+// stay as aliases — they log a one-time deprecation warning on first use
+// and are removed in Phase 7.
+
+const handlers = require('./handlers');
+
+module.exports = [
+  {
+    topic: 'data.clock',
+    aliases: ['clock'],
+    payloadSchema: { type: 'any' },
+    handler: handlers.dataClock,
+  },
+  {
+    topic: 'data.fluent',
+    aliases: ['Fluent'],
+    payloadSchema: { type: 'object' },
+    handler: handlers.dataFluent,
+  },
+  {
+    topic: 'data.otr',
+    aliases: ['OTR'],
+    payloadSchema: { type: 'any' },
+    handler: handlers.dataOTR,
+  },
+  {
+    topic: 'data.temperature',
+    aliases: ['Temperature'],
+    payloadSchema: { type: 'any' },
+    handler: handlers.dataTemperature,
+  },
+  {
+    topic: 'data.dispersion',
+    aliases: ['Dispersion'],
+    payloadSchema: { type: 'any' },
+    handler: handlers.dataDispersion,
+  },
+  {
+    topic: 'child.register',
+    aliases: ['registerChild'],
+    payloadSchema: { type: 'any' },
+    handler: handlers.childRegister,
+  },
+];

src/kinetics/baseEngine.js

@@ -0,0 +1,139 @@
+'use strict';
+
+const EventEmitter = require('events');
+const ASM3 = require('../reaction_modules/asm3_class.js');
+const { create, all } = require('mathjs');
+const { childRegistrationUtils, logger, MeasurementContainer, POSITIONS } = require('generalFunctions');
+
+const math = create(all, { matrix: 'Array' });
+
+const S_O_INDEX = 0;
+const NUM_SPECIES = 13;
+
+// Abstract reactor engine. Holds the influent/OTR/temperature state plus
+// the parent-side child registration that the original Reactor class
+// exposed. Concrete CSTR / PFR subclasses provide tick().
+class BaseReactorEngine {
+  constructor(config) {
+    this.config = config;
+    this.logger = new logger(
+      this.config.general.logging.enabled,
+      this.config.general.logging.logLevel,
+      config.general.name,
+    );
+    this.emitter = new EventEmitter();
+    this.measurements = new MeasurementContainer();
+    this.upstreamReactor = null;
+    this.childRegistrationUtils = new childRegistrationUtils(this);
+
+    this.asm = new ASM3();
+    this.volume = config.volume;
+
+    this.Fs = Array(config.n_inlets).fill(0);
+    this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0));
+    this.OTR = 0.0;
+    this.temperature = 20;
+
+    this.kla = config.kla;
+    this.currentTime = Date.now();
+    // timeStep stored in days (the integrator uses [d] internally).
+    this.timeStep = (1 / (24 * 60 * 60)) * this.config.timeStep;
+    this.speedUpFactor = config.speedUpFactor ?? 1;
+  }
+
+  set setInfluent(input) {
+    const index_in = input.payload.inlet;
+    this.Fs[index_in] = input.payload.F;
+    this.Cs_in[index_in] = input.payload.C;
+  }
+
+  set setOTR(input) { this.OTR = input.payload; }
+
+  set setTemperature(input) {
+    const p = input?.payload;
+    const raw = (p && typeof p === 'object' && p.value !== undefined) ? p.value : p;
+    const v = Number(raw);
+    if (!Number.isFinite(v)) { this.logger.warn(`Invalid temperature input: ${raw}`); return; }
+    this.temperature = v;
+  }
+
+  get getEffluent() {
+    const last = Array.isArray(this.state.at?.(-1)) ? this.state.at(-1) : this.state;
+    return { topic: 'Fluent', payload: { inlet: 0, F: math.sum(this.Fs), C: last }, timestamp: this.currentTime };
+  }
+
+  get getGridProfile() { return null; }
+
+  _calcOTR(S_O, T = 20.0) {
+    const sat = this._calcOxygenSaturation(T);
+    return this.kla * (sat - S_O);
+  }
+
+  _calcOxygenSaturation(T = 20.0) {
+    return 14.652 - 4.1022e-1 * T + 7.9910e-3 * T * T + 7.7774e-5 * T * T * T;
+  }
+
+  _capDissolvedOxygen(state) {
+    const sat = this._calcOxygenSaturation(this.temperature);
+    const capRow = (row) => {
+      if (!Array.isArray(row)) return row;
+      const next = row.slice();
+      if (Number.isFinite(next[S_O_INDEX])) next[S_O_INDEX] = Math.max(0, Math.min(next[S_O_INDEX], sat));
+      return next;
+    };
+    return (Array.isArray(state) && Array.isArray(state[0])) ? state.map(capRow) : capRow(state);
+  }
+
+  _arrayClip2Zero(arr) {
+    if (Array.isArray(arr)) return arr.map((x) => this._arrayClip2Zero(x));
+    return arr < 0 ? 0 : arr;
+  }
+
+  registerChild(child, softwareType) {
+    switch (softwareType) {
+      case 'measurement': this._connectMeasurement(child); break;
+      case 'reactor':     this._connectReactor(child);     break;
+      default:            this.logger.error(`Unrecognized softwareType: ${softwareType}`);
+    }
+  }
+
+  _connectMeasurement(measurement) {
+    if (!measurement) { this.logger.warn('Invalid measurement provided.'); return; }
+    const fn = measurement.config.functionality;
+    const position = fn.distance !== 'undefined' ? fn.distance : fn.positionVsParent;
+    const measurementType = measurement.config.asset.type;
+    const eventName = `${measurementType}.measured.${position}`;
+    measurement.measurements.emitter.on(eventName, (eventData) => {
+      this.measurements
+        .type(measurementType).variant('measured').position(position)
+        .value(eventData.value, eventData.timestamp, eventData.unit);
+      this._updateMeasurement(measurementType, eventData.value, position, eventData);
+    });
+  }
+
+  _connectReactor(reactor) {
+    if (!reactor) { this.logger.warn('Invalid reactor provided.'); return; }
+    this.upstreamReactor = reactor;
+    reactor.emitter.on('stateChange', (data) => this.updateState(data));
+  }
+
+  _updateMeasurement(measurementType, value, position) {
+    if (measurementType === 'temperature' && position === POSITIONS.AT_EQUIPMENT) {
+      this.temperature = value;
+      return;
+    }
+    this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
+  }
+
+  updateState(newTime = Date.now()) {
+    const day2ms = 1000 * 60 * 60 * 24;
+    if (this.upstreamReactor) this.setInfluent = this.upstreamReactor.getEffluent;
+    const n_iter = Math.floor(this.speedUpFactor * (newTime - this.currentTime) / (this.timeStep * day2ms));
+    if (!n_iter) return;
+    for (let n = 0; n < n_iter; n += 1) this.tick(this.timeStep);
+    this.currentTime += (n_iter * this.timeStep * day2ms) / this.speedUpFactor;
+    this.emitter.emit('stateChange', this.currentTime);
+  }
+}
+
+module.exports = { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES };

src/kinetics/cstr.js

@@ -0,0 +1,27 @@
+'use strict';
+
+const { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES } = require('./baseEngine.js');
+
+class Reactor_CSTR extends BaseReactorEngine {
+  constructor(config) {
+    super(config);
+    this.state = config.initialState;
+  }
+
+  // Forward Euler step over `time_step` days.
+  tick(time_step) {
+    const inflow  = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
+    const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
+    const reaction = this.asm.compute_dC(this.state, this.temperature);
+    const transfer = Array(NUM_SPECIES).fill(0.0);
+    transfer[S_O_INDEX] = isNaN(this.kla)
+      ? this.OTR
+      : this._calcOTR(this.state[S_O_INDEX], this.temperature);
+
+    const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step);
+    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(math.add(this.state, dC_total)));
+    return this.state;
+  }
+}
+
+module.exports = Reactor_CSTR;

src/kinetics/pfr.js

@@ -0,0 +1,132 @@
+'use strict';
+
+const { assertNoNaN } = require('../utils.js');
+const { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES } = require('./baseEngine.js');
+
+class Reactor_PFR extends BaseReactorEngine {
+  constructor(config) {
+    super(config);
+
+    this.length = config.length;
+    this.n_x = config.resolution_L;
+    this.d_x = this.length / this.n_x;
+    this.A = this.volume / this.length;
+    this.alpha = config.alpha;
+
+    this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
+    this.D = 0.0;
+
+    this.D_op  = this._makeDoperator(true, true);
+    this.D2_op = this._makeD2operator();
+    assertNoNaN(this.D_op,  'Derivative operator');
+    assertNoNaN(this.D2_op, 'Second derivative operator');
+  }
+
+  get getGridProfile() {
+    return {
+      grid: this.state.map((row) => row.slice()),
+      n_x: this.n_x,
+      d_x: this.d_x,
+      length: this.length,
+      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: this.currentTime,
+    };
+  }
+
+  set setDispersion(input) { this.D = input.payload; }
+
+  updateState(newTime) {
+    super.updateState(newTime);
+    const Pe_local = (this.d_x * math.sum(this.Fs)) / (this.D * this.A);
+    const Co_D = (this.D * this.timeStep) / (this.d_x * this.d_x);
+    if (Pe_local >= 2)  this.logger.warn(`Local Peclet number (${Pe_local}) is too high! Increase reactor resolution.`);
+    if (Co_D >= 0.5)    this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
+  }
+
+  // Explicit finite-difference step over `time_step` days.
+  tick(time_step) {
+    const dispersion = math.multiply(this.D / (this.d_x * this.d_x), this.D2_op, this.state);
+    const advection  = math.multiply(-1 * math.sum(this.Fs) / (this.A * this.d_x), this.D_op, this.state);
+    const reaction   = this.state.map((slice) => this.asm.compute_dC(slice, this.temperature));
+    const transfer   = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
+
+    const klaIsNaN = isNaN(this.kla);
+    for (let i = 1; i < this.n_x - 1; i += 1) {
+      const otr = klaIsNaN ? this.OTR : this._calcOTR(this.state[i][S_O_INDEX], this.temperature);
+      transfer[i][S_O_INDEX] = otr * this.n_x / (this.n_x - 2);
+    }
+
+    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
+    const stateNew = math.add(this.state, dC_total);
+    this._applyBoundaryConditions(stateNew);
+    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
+    return stateNew;
+  }
+
+  _updateMeasurement(measurementType, value, position, context) {
+    if (measurementType === 'quantity (oxygen)') {
+      if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) {
+        this.logger.warn(`Ignoring oxygen measurement update with invalid data (position=${position}, value=${value}).`);
+        return;
+      }
+      const rawIndex = Math.round((position / this.config.length) * this.n_x);
+      const grid_pos = Math.max(0, Math.min(this.n_x - 1, rawIndex));
+      this.state[grid_pos][S_O_INDEX] = value;
+      return;
+    }
+    super._updateMeasurement(measurementType, value, position, context);
+  }
+
+  // Generalised Danckwerts at inlet when flow > 0; Neumann (no-flux) at outlet
+  // and at inlet when there is no flow.
+  _applyBoundaryConditions(state) {
+    if (math.sum(this.Fs) > 0) {
+      const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
+      const BC_disp = ((1 - this.alpha) * this.D * this.A) / (math.sum(this.Fs) * this.d_x);
+      state[0] = math.multiply(1 / (1 + BC_disp), math.add(BC_C_in, math.multiply(BC_disp, state[1])));
+    } else {
+      state[0] = state[1];
+    }
+    state[this.n_x - 1] = state[this.n_x - 2];
+  }
+
+  _makeDoperator(central = false, higher_order = false) {
+    if (higher_order) {
+      if (!central) throw new Error('Upwind higher order method not implemented! Use central scheme instead.');
+      const I = math.resize(math.diag(Array(this.n_x).fill(1 / 12), -2),  [this.n_x, this.n_x]);
+      const A = math.resize(math.diag(Array(this.n_x).fill(-2 / 3), -1), [this.n_x, this.n_x]);
+      const B = math.resize(math.diag(Array(this.n_x).fill(2 / 3),  1),  [this.n_x, this.n_x]);
+      const C = math.resize(math.diag(Array(this.n_x).fill(-1 / 12), 2), [this.n_x, this.n_x]);
+      const D = math.add(I, A, B, C);
+      // Preserve the pre-refactor aliasing: D[1] = NearBoundary; NearBoundary.reverse()
+      // mutates D[1] in place; then D[n_x-2] = -1 * NearBoundary uses the reversed view.
+      const nb = Array(this.n_x).fill(0.0);
+      nb[0] = -1 / 4; nb[1] = -5 / 6; nb[2] = 3 / 2; nb[3] = -1 / 2; nb[4] = 1 / 12;
+      D[1] = nb;
+      nb.reverse();
+      D[this.n_x - 2] = math.multiply(-1, nb);
+      D[0] = Array(this.n_x).fill(0);
+      D[this.n_x - 1] = Array(this.n_x).fill(0);
+      return D;
+    }
+    const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1 + central)), central),  [this.n_x, this.n_x]);
+    const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1 + central)), -1),       [this.n_x, this.n_x]);
+    const D = math.add(I, A);
+    D[0] = Array(this.n_x).fill(0);
+    D[this.n_x - 1] = Array(this.n_x).fill(0);
+    return D;
+  }
+
+  _makeD2operator() {
+    const I = math.diag(Array(this.n_x).fill(-2), 0);
+    const A = math.resize(math.diag(Array(this.n_x).fill(1),  1),  [this.n_x, this.n_x]);
+    const B = math.resize(math.diag(Array(this.n_x).fill(1), -1),  [this.n_x, this.n_x]);
+    const D2 = math.add(I, A, B);
+    D2[0] = Array(this.n_x).fill(0);
+    D2[this.n_x - 1] = Array(this.n_x).fill(0);
+    return D2;
+  }
+}
+
+module.exports = Reactor_PFR;

src/nodeClass.js

@@ -1,208 +1,53 @@
-const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
-const { outputUtils, configManager } = require('generalFunctions');
+'use strict';
 
-const REACTOR_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'
-];
+const { BaseNodeAdapter } = require('generalFunctions');
+const Reactor = require('./specificClass.js');
+const commands = require('./commands');
 
+const 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'];
 
-class nodeClass {
-    /**
-    * Node-RED node class for advanced-reactor.
-    * @param {object} uiConfig - Node-RED node configuration
-    * @param {object} RED - Node-RED runtime API
-    * @param {object} nodeInstance - Node-RED node instance
-    * @param {string} nameOfNode - Name of the node
-    */
-    constructor(uiConfig, RED, nodeInstance, nameOfNode) {
-        // Preserve RED reference for HTTP endpoints if needed
-        this.node = nodeInstance;
-        this.RED = RED;
-        this.name = nameOfNode;
-        this.source = null;
+class nodeClass extends BaseNodeAdapter {
+  static DomainClass = Reactor;
+  static commands = commands;
+  // Tick-driven: ASM kinetics integrate over wall-clock time. The engine's
+  // updateState computes how many internal Euler/FD steps fit in the elapsed
+  // ms; without a periodic tick the integrator never advances.
+  static tickInterval = 1000;
+  static statusInterval = 1000;
 
-        this._loadConfig(uiConfig)
-        this._setupClass();
-        this._output = new outputUtils();
+  buildDomainConfig(uiConfig) {
+    const initialState = {};
+    for (const k of SPECIES) initialState[k] = parseFloat(uiConfig[`${k}_init`]);
+    return {
+      reactor: {
+        reactor_type: uiConfig.reactor_type,
+        volume:       parseFloat(uiConfig.volume),
+        length:       parseFloat(uiConfig.length),
+        resolution_L: parseInt(uiConfig.resolution_L, 10),
+        alpha:        parseFloat(uiConfig.alpha),
+        n_inlets:     parseInt(uiConfig.n_inlets, 10),
+        kla:          parseFloat(uiConfig.kla),
+        timeStep:     parseFloat(uiConfig.timeStep),
+        speedUpFactor: Number(uiConfig.speedUpFactor) || 1,
+      },
+      initialState,
+    };
+  }
 
-        this._attachInputHandler();
-        this._registerChild();
-        this._startTickLoop();
-        this._attachCloseHandler();
-    }
-
-    /**
-     * Handle node-red input messages
-     */
-    _attachInputHandler() {
-        this.node.on('input', (msg, send, done) => {
-            try {
-                switch (msg.topic) {
-                    case "clock":
-                        this.source.updateState(msg.timestamp);
-                        send([msg, null, null]);
-                        break;
-                    case "Fluent":
-                        this.source.setInfluent = msg;
-                        break;
-                    case "OTR":
-                        this.source.setOTR = msg;
-                        break;
-                    case "Temperature":
-                        this.source.setTemperature = msg;
-                        break;
-                    case "Dispersion":
-                        this.source.setDispersion = msg;
-                        break;
-                    case 'registerChild': {
-                        const childId = msg.payload;
-                        const childObj = this.RED.nodes.getNode(childId);
-                        if (!childObj || !childObj.source) {
-                            this.source?.logger?.warn(`registerChild skipped: missing child/source for id=${childId}`);
-                            break;
-                        }
-                        this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
-                        break;
-                    }
-                    default:
-                        this.source?.logger?.warn(`Unknown topic: ${msg.topic}`);
-                }
-            } catch (error) {
-                this.source?.logger?.error(`Input handler failure: ${error.message}`);
-            }
-
-            if (typeof done === 'function') {
-                done();
-            }
-        });
-    }
-
-    /**
-     * Parse node configuration using ConfigManager
-     * @param {object} uiConfig Config set in UI in node-red
-     */
-    _loadConfig(uiConfig) {
-        const cfgMgr = new configManager();
-
-        // Build config: base sections + reactor-specific domain config
-        this.config = cfgMgr.buildConfig('reactor', uiConfig, this.node.id, {
-            reactor_type: uiConfig.reactor_type,
-            volume: parseFloat(uiConfig.volume),
-            length: parseFloat(uiConfig.length),
-            resolution_L: parseInt(uiConfig.resolution_L),
-            alpha: parseFloat(uiConfig.alpha),
-            n_inlets: parseInt(uiConfig.n_inlets),
-            kla: parseFloat(uiConfig.kla),
-            initialState: [
-                parseFloat(uiConfig.S_O_init),
-                parseFloat(uiConfig.S_I_init),
-                parseFloat(uiConfig.S_S_init),
-                parseFloat(uiConfig.S_NH_init),
-                parseFloat(uiConfig.S_N2_init),
-                parseFloat(uiConfig.S_NO_init),
-                parseFloat(uiConfig.S_HCO_init),
-                parseFloat(uiConfig.X_I_init),
-                parseFloat(uiConfig.X_S_init),
-                parseFloat(uiConfig.X_H_init),
-                parseFloat(uiConfig.X_STO_init),
-                parseFloat(uiConfig.X_A_init),
-                parseFloat(uiConfig.X_TS_init)
-            ],
-            timeStep: parseFloat(uiConfig.timeStep),
-            speedUpFactor: Number(uiConfig.speedUpFactor) || 1
-        });
-    }
-
-    /**
-     * Register this node as a child upstream and downstream.
-     * Delayed to avoid Node-RED startup race conditions.
-     */
-    _registerChild() {
-        setTimeout(() => {
-        this.node.send([
-            null,
-            null,
-            { topic: 'registerChild', payload: this.node.id, positionVsParent: this.config?.functionality?.positionVsParent || 'atEquipment' }
-        ]);
-        }, 100);
-    }
-
-    /**
-     * Setup reactor class based on config
-     */
-    _setupClass() {
-        let new_reactor;
-
-        switch (this.config.reactor_type) {
-            case "CSTR":
-                new_reactor = new Reactor_CSTR(this.config);
-                break;
-            case "PFR":
-                new_reactor = new Reactor_PFR(this.config);
-                break;
-            default:
-                this.node.warn("Unknown reactor type: " + this.config.reactor_type + ". Falling back to CSTR.");
-                new_reactor = new Reactor_CSTR(this.config);
-        }
-
-        this.source = new_reactor; // protect from reassignment
-        this.node.source = this.source;
-    }
-
-    _startTickLoop() {
-        setTimeout(() => {
-            this._tickInterval = setInterval(() => this._tick(), 1000);
-        }, 1000);
-    }
-
-    _tick(){
-        const gridProfile = this.source.getGridProfile;
-        if (gridProfile) {
-            this.node.send([{ topic: "GridProfile", payload: gridProfile }, null, null]);
-        }
-        this.node.send([this.source.getEffluent, this._buildTelemetryMessage(), null]);
-    }
-
-    _buildTelemetryMessage() {
-        const effluent = this.source?.getEffluent;
-        const concentrations = effluent?.payload?.C;
-        if (!Array.isArray(concentrations)) {
-            return null;
-        }
-
-        const telemetry = {
-            flow_total: Number(effluent.payload.F),
-            temperature: Number(this.source?.temperature),
-        };
-
-        for (let i = 0; i < Math.min(REACTOR_SPECIES.length, concentrations.length); i += 1) {
-            const value = Number(concentrations[i]);
-            if (Number.isFinite(value)) {
-                telemetry[REACTOR_SPECIES[i]] = value;
-            }
-        }
-
-        return this._output.formatMsg(telemetry, this.config, 'influxdb');
-    }
-
-    _attachCloseHandler() {
-        this.node.on('close', (done) => {
-            clearInterval(this._tickInterval);
-            if (typeof done === 'function') done();
-        });
-    }
+  // The kinetics engine drives Port-0 effluent + grid-profile shapes that
+  // don't fit BaseNodeAdapter's delta-compressed payload. Override the
+  // periodic emission so the Fluent / GridProfile contract is preserved.
+  _emitOutputs() {
+    const src = this.source;
+    if (!src?.engine) return;
+    src.updateState(Date.now());
+    const grid = src.getGridProfile;
+    if (grid) this.node.send([{ topic: 'GridProfile', payload: grid }, null, null]);
+    const raw = src.getOutput();
+    const influx = this._output.formatMsg(raw, src.config || this.config, 'influxdb');
+    this.node.send([src.getEffluent, influx, null]);
+  }
 }
 
 module.exports = nodeClass;

src/specificClass.js

@@ -1,481 +1,134 @@
-const ASM3 = require('./reaction_modules/asm3_class.js');
-const { create, all, isArray } = require('mathjs');
-const { assertNoNaN } = require('./utils.js');
-const { childRegistrationUtils, logger, MeasurementContainer, POSITIONS } = require('generalFunctions');
-const EventEmitter = require('events');
+'use strict';
 
-const mathConfig = {
-  matrix: 'Array' // use Array as the matrix type
-};
+const { BaseDomain, statusBadge, POSITIONS } = require('generalFunctions');
+const Reactor_CSTR = require('./kinetics/cstr.js');
+const Reactor_PFR  = require('./kinetics/pfr.js');
 
-const math = create(all, mathConfig);
+const SPECIES_KEYS = ['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'];
 
-const S_O_INDEX = 0;
-const NUM_SPECIES = 13;
-const DEBUG = false;
+// Reactor — biological reactor orchestrator (Unit-level). Wraps a CSTR or
+// PFR kinetics engine and exposes the BaseDomain surface to BaseNodeAdapter.
+// The engines own the ASM3 integration; this class wires child registration
+// through ChildRouter, holds the validated config, and presents getOutput /
+// getStatusBadge.
+class Reactor extends BaseDomain {
+  static name = 'reactor';
 
-class Reactor {
-  /**
-   * Reactor base class.
-   * @param {object} config - Configuration object containing reactor parameters.
-   */
-  constructor(config) {
-    this.config = config;
-    // EVOLV stuff
-    this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name);
-    this.emitter = new EventEmitter();
-    this.measurements = new MeasurementContainer();
-    this.upstreamReactor = null;
-    this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
+  configure() {
+    const flat = this._flattenEngineConfig(this.config);
+    this.engine = this._buildEngine(flat);
 
-    this.asm = new ASM3();
+    // Re-emit upstream-reactor stateChange and engine stateChange events on
+    // the BaseDomain emitter so adapter listeners pick them up uniformly.
+    this.engine.emitter.on('stateChange', (t) => this.emitter.emit('stateChange', t));
 
-    this.volume = config.volume; // fluid volume reactor [m3]
+    // ChildRouter dispatches to engine handlers — keeps the existing
+    // _connectMeasurement / _connectReactor wiring intact, just centralised.
+    this.router.onRegister('measurement', (child) => this.engine._connectMeasurement(child));
+    this.router.onRegister('reactor',     (child) => this.engine._connectReactor(child));
 
-    this.Fs = Array(config.n_inlets).fill(0); // fluid debits per inlet [m3 d-1]
-    this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0)); // composition influents
-    this.OTR = 0.0; // oxygen transfer rate [g O2 d-1 m-3]
-    this.temperature = 20; // temperature [C]
-
-    this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
-
-    this.currentTime = Date.now(); // milliseconds since epoch [ms]
-    this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
-    this.speedUpFactor = config.speedUpFactor ?? 1; // speed up factor for simulation
+    // Bridge engine.measurements into the BaseDomain measurements container
+    // so getFlattenedOutput surfaces temperature / oxygen series.
+    this.measurements = this.engine.measurements;
   }
 
-  /**
-   * Setter for influent data.
-   * @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
-  */
-  set setInfluent(input) {
-    let index_in = input.payload.inlet;
-    this.Fs[index_in] = input.payload.F;
-    this.Cs_in[index_in] = input.payload.C;
-  }
-
-  /**
-   * Setter for OTR (Oxygen Transfer Rate).
-   * @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1 m-3].
-   */
-  set setOTR(input) {
-    this.OTR = input.payload;
-  }
-
-  /**
-   * Setter for reactor temperature [C].
-   * Accepts either a direct numeric payload or { value } object payload.
-   * @param {object} input - Input object (msg)
-   */
-  set setTemperature(input) {
-    const payload = input?.payload;
-    const rawValue = (payload && typeof payload === 'object' && payload.value !== undefined)
-      ? payload.value
-      : payload;
-    const parsedValue = Number(rawValue);
-    if (!Number.isFinite(parsedValue)) {
-      this.logger.warn(`Invalid temperature input: ${rawValue}`);
-      return;
-    }
-    this.temperature = parsedValue;
-  }
-
-  /**
-   * Getter for effluent data.
-   * @returns {object} Effluent data object (msg), defaults to inlet 0.
-   */
-  get getEffluent() { // getter for Effluent, defaults to inlet 0
-    if (isArray(this.state.at(-1))) {
-      return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
-    }
-    return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
-  }
-
-  get getGridProfile() { return null; }
-
-  /**
-   * Calculate the oxygen transfer rate (OTR) based on the dissolved oxygen concentration and temperature.
-   * @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
-   * @param {number} T - Temperature in Celsius, default to 20 C.
-   * @returns {number} - Calculated OTR [g O2 d-1 m-3].
-   */
-  _calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C
-    let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
-    return this.kla * (S_O_sat - S_O);
-  }
-
-  _calcOxygenSaturation(T = 20.0) {
-    return 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
-  }
-
-  _capDissolvedOxygen(state) {
-    const saturation = this._calcOxygenSaturation(this.temperature);
-    const capRow = (row) => {
-      if (!Array.isArray(row)) {
-        return row;
-      }
-      const next = row.slice();
-      if (Number.isFinite(next[S_O_INDEX])) {
-        next[S_O_INDEX] = Math.max(0, Math.min(next[S_O_INDEX], saturation));
-      }
-      return next;
-    };
-
-    if (Array.isArray(state) && Array.isArray(state[0])) {
-      return state.map(capRow);
-    }
-    return capRow(state);
-  }
-
-  /**
-   * Clip values in an array to zero.
-   * @param {Array} arr - Array of values to clip.
-   * @returns {Array} - New array with values clipped to zero.
-   */
-  _arrayClip2Zero(arr) {
-    if (Array.isArray(arr)) {
-      return arr.map(x => this._arrayClip2Zero(x));
-    } else {
-      return arr < 0 ? 0 : arr;
-    }
-  }
-
-  registerChild(child, softwareType) {
-    switch (softwareType) {
-      case "measurement":
-        this.logger.debug(`Registering measurement child.`);
-        this._connectMeasurement(child);
-        break;
-      case "reactor":
-        this.logger.debug(`Registering reactor child.`);
-        this._connectReactor(child);
-        break;
-
-      default:
-        this.logger.error(`Unrecognized softwareType: ${softwareType}`);
-    }
-  }
-
-  _connectMeasurement(measurement) {
-    if (!measurement) {
-      this.logger.warn("Invalid measurement provided.");
-      return;
-    }
-
-    let position;
-    if (measurement.config.functionality.distance !== 'undefined') {
-      position = measurement.config.functionality.distance;
-    } else {
-      position = measurement.config.functionality.positionVsParent;
-    }
-    const measurementType = measurement.config.asset.type;
-    const eventName = `${measurementType}.measured.${position}`;
-
-    // Register event listener for measurement updates
-    measurement.measurements.emitter.on(eventName, (eventData) => {
-      this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
-
-      // Store directly in parent's measurement container
-      this.measurements
-        .type(measurementType)
-        .variant("measured")
-        .position(position)
-        .value(eventData.value, eventData.timestamp, eventData.unit);
-
-      this._updateMeasurement(measurementType, eventData.value, position, eventData);
-    });
-  }
-
-
-  _connectReactor(reactor) {
-    if (!reactor) {
-      this.logger.warn("Invalid reactor provided.");
-      return;
-    }
-
-    this.upstreamReactor = reactor;
-
-    reactor.emitter.on("stateChange", (data) => {
-      this.logger.debug(`State change of upstream reactor detected.`);
-      this.updateState(data);
-    });
-  }
-
-
-  _updateMeasurement(measurementType, value, position, _context) {
-    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
-    switch (measurementType) {
-      case "temperature":
-        if (position == POSITIONS.AT_EQUIPMENT) {
-          this.temperature = value;
-        }
-        break;
-      default:
-        this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
-        return;
-    }
-  }
-
-  /**
-   * Update the reactor state based on the new time.
-   * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
-   */
-  updateState(newTime = Date.now()) { // expect update with timestamp
-    const day2ms = 1000 * 60 * 60 * 24;
-
-    if (this.upstreamReactor) {
-      this.setInfluent = this.upstreamReactor.getEffluent;
-    }
-
-    let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms));
-    if (n_iter) {
-      let n = 0;
-      while (n < n_iter) {
-        this.tick(this.timeStep);
-        n += 1;
-      }
-      this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor;
-      this.emitter.emit("stateChange", this.currentTime);
-    }
-  }
-}
-
-class Reactor_CSTR extends Reactor {
-  /**
-   * Reactor_CSTR class for Continuous Stirred Tank Reactor.
-   * @param {object} config - Configuration object containing reactor parameters.
-   */
-  constructor(config) {
-      super(config);
-      this.state = config.initialState;
-  }
-
-  /**
-   * Tick the reactor state using the forward Euler method.
-   * @param {number} time_step - Time step for the simulation [d].
-   * @returns {Array} - New reactor state.
-   */
-  tick(time_step) { // tick reactor state using forward Euler method
-    const inflow = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
-    const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
-    const reaction = this.asm.compute_dC(this.state, this.temperature);
-    const transfer = Array(NUM_SPECIES).fill(0.0);
-    transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
-
-    const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step)
-    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(math.add(this.state, dC_total))); // clip concentrations and enforce physical DO saturation
-    if(DEBUG){
-      assertNoNaN(dC_total, "change in state");
-      assertNoNaN(this.state, "new state");
-    }
-    return this.state;
-  }
-}
-
-class Reactor_PFR extends Reactor {
-  /**
-   * Reactor_PFR class for Plug Flow Reactor.
-   * @param {object} config - Configuration object containing reactor parameters.
-   */
-  constructor(config) {
-    super(config);
-
-    this.length = config.length; // reactor length [m]
-    this.n_x = config.resolution_L; // number of slices
-
-    this.d_x = this.length / this.n_x;
-    this.A = this.volume / this.length; // crosssectional area [m2]
-
-    this.alpha = config.alpha;
-
-    this.state = Array.from(Array(this.n_x), () => config.initialState.slice())
-
-    this.D = 0.0; // axial dispersion [m2 d-1]
-
-    this.D_op = this._makeDoperator(true, true);
-    assertNoNaN(this.D_op, "Derivative operator");
-
-    this.D2_op = this._makeD2operator();
-    assertNoNaN(this.D2_op, "Second derivative operator");
-  }
-
-  get getGridProfile() {
+  // Translate the nested schema config (reactor.*, initialState.*) into the
+  // flat shape the kinetics engines accept.
+  _flattenEngineConfig(config) {
+    const reactor = config.reactor || {};
+    const init = config.initialState || {};
+    const initialState = SPECIES_KEYS.map((k) => Number(init[k] ?? 0));
     return {
-      grid: this.state.map(row => row.slice()),
-      n_x: this.n_x,
-      d_x: this.d_x,
-      length: this.length,
-      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: this.currentTime
+      general: config.general,
+      functionality: config.functionality,
+      reactor_type: reactor.reactor_type ?? 'CSTR',
+      volume: Number(reactor.volume),
+      length: Number(reactor.length),
+      resolution_L: Number(reactor.resolution_L),
+      alpha: Number(reactor.alpha),
+      n_inlets: Number(reactor.n_inlets),
+      kla: Number(reactor.kla),
+      timeStep: Number(reactor.timeStep),
+      speedUpFactor: Number(reactor.speedUpFactor) || 1,
+      initialState,
     };
   }
 
-  /**
-   * Setter for axial dispersion.
-   * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
-   */
-  set setDispersion(input) {
-    this.D = input.payload;
-  }
-
-  updateState(newTime) {
-    super.updateState(newTime);
-    let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
-    let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
-
-    (Pe_local >= 2) && this.logger.warn(`Local Peclet number (${Pe_local}) is too high! Increase reactor resolution.`);
-    (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
-
-    if(DEBUG) {
-      console.log("Inlet state max " + math.max(this.state[0]))
-      console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A));
-      console.log("Pe local " + Pe_local);
-      console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x));
-      console.log("Co D " + Co_D);
-    }
-  }
-
-  /**
-   * Tick the reactor state using explicit finite difference method.
-   * @param {number} time_step - Time step for the simulation [d].
-   * @returns {Array} - New reactor state.
-   */
-  tick(time_step) {
-    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.state);
-    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.state);
-    const reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
-    const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
-
-    if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
-      for (let i = 1; i < this.n_x - 1; i++) {
-        transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
-      }
-    } else {
-    for (let i = 1; i < this.n_x - 1; i++) {
-        transfer[i][S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
-      }
-    }
-
-    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
-
-    const stateNew = math.add(this.state, dC_total);
-    this._applyBoundaryConditions(stateNew);
-
-    if (DEBUG) {
-      assertNoNaN(dispersion, "dispersion");
-      assertNoNaN(advection, "advection");
-      assertNoNaN(reaction, "reaction");
-      assertNoNaN(dC_total, "change in state");
-      assertNoNaN(stateNew, "new state post BC");
-    }
-
-    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
-    return stateNew;
-  }
-
-  _updateMeasurement(measurementType, value, position, context) {
-    switch(measurementType) {
-      case "quantity (oxygen)":
-        if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) {
-          this.logger.warn(`Ignoring oxygen measurement update with invalid data (position=${position}, value=${value}).`);
-          break;
-        }
-        {
-          // Clamp sensor-derived position to valid PFR grid bounds.
-          const rawIndex = Math.round(position / this.config.length * this.n_x);
-          const grid_pos = Math.max(0, Math.min(this.n_x - 1, rawIndex));
-          this.state[grid_pos][S_O_INDEX] = value; // reconcile measured oxygen concentration into nearest grid cell
-        }
-        break;
+  _buildEngine(flat) {
+    // The schema enum validator lowercases the configured value, so accept
+    // either case.
+    switch (String(flat.reactor_type || '').toUpperCase()) {
+      case 'CSTR': return new Reactor_CSTR(flat);
+      case 'PFR':  return new Reactor_PFR(flat);
       default:
-        super._updateMeasurement(measurementType, value, position, context);
+        this.logger.warn(`Unknown reactor type: ${flat.reactor_type}. Falling back to CSTR.`);
+        return new Reactor_CSTR(flat);
     }
   }
 
-  /**
-   * Apply boundary conditions to the reactor state.
-   *  for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux
-   *  for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
-   * @param {Array} state - Current reactor state without enforced BCs.
-   */
-  _applyBoundaryConditions(state) {
-    if (math.sum(this.Fs) > 0) { // Danckwerts BC
-      const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
-      const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
-      state[0] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, state[1])));
-    } else {
-      state[0] = state[1];
-    }
-    // Neumann BC (no flux)
-    state[this.n_x-1] = state[this.n_x-2];
+  // Adapter input setters — forwarded straight to the engine.
+  set setInfluent(msg)    { this.engine.setInfluent = msg; }
+  set setOTR(msg)         { this.engine.setOTR = msg; }
+  set setTemperature(msg) { this.engine.setTemperature = msg; }
+  set setDispersion(msg)  { if (this.engine instanceof Reactor_PFR) this.engine.setDispersion = msg; }
+
+  updateState(t) { this.engine.updateState(t); this.notifyOutputChanged(); }
+
+  // Engine pass-through — needed so the BaseNodeAdapter tick loop (and
+  // tests calling reactor.tick(dt) directly) drive the ASM integration.
+  // Without this the Node-RED tick fires `source.tick?.()`, gets undefined,
+  // and the kinetics state never advances.
+  tick(timeStep) {
+    const result = this.engine.tick(timeStep);
+    this.notifyOutputChanged();
+    return result;
   }
 
-  /**
-   * Create finite difference first derivative operator.
-   * @param {boolean} central - Use central difference scheme if true, otherwise use upwind scheme.
-   * @param {boolean} higher_order - Use higher order scheme if true, otherwise use first order scheme.
-   * @returns {Array} - First derivative operator matrix.
-   */
-  _makeDoperator(central = false, higher_order = false) { // create gradient operator
-    if (higher_order) {
-      if (central) {
-        const I = math.resize(math.diag(Array(this.n_x).fill(1/12), -2), [this.n_x, this.n_x]);
-        const A = math.resize(math.diag(Array(this.n_x).fill(-2/3), -1), [this.n_x, this.n_x]);
-        const B = math.resize(math.diag(Array(this.n_x).fill(2/3), 1), [this.n_x, this.n_x]);
-        const C = math.resize(math.diag(Array(this.n_x).fill(-1/12), 2), [this.n_x, this.n_x]);
-        const D = math.add(I, A, B, C);
-        const NearBoundary = Array(this.n_x).fill(0.0);
-        NearBoundary[0] = -1/4;
-        NearBoundary[1] = -5/6;
-        NearBoundary[2] = 3/2;
-        NearBoundary[3] = -1/2;
-        NearBoundary[4] = 1/12;
-        D[1] = NearBoundary;
-        NearBoundary.reverse();
-        D[this.n_x-2] = math.multiply(-1, NearBoundary);
-        D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
-        D[this.n_x-1] = Array(this.n_x).fill(0);
-        return D;
-      } else {
-        throw new Error("Upwind higher order method not implemented! Use central scheme instead.");
-      }
-    } else {
-      const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1+central)), central), [this.n_x, this.n_x]);
-      const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1+central)), -1), [this.n_x, this.n_x]);
-      const D = math.add(I, A);
-      D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
-      D[this.n_x-1] = Array(this.n_x).fill(0);
-      return D;
+  get getEffluent()    { return this.engine.getEffluent; }
+  get getGridProfile() { return this.engine.getGridProfile; }
+  get temperature()    { return this.engine.temperature; }
+
+  // Per-tick output for Port 0 / Port 1. Carries the effluent vector plus
+  // a flat per-species block keyed by SPECIES_KEYS for InfluxDB telemetry.
+  getOutput() {
+    const eff = this.engine.getEffluent;
+    const C = Array.isArray(eff?.payload?.C) ? eff.payload.C : [];
+    const out = {
+      flow_total: Number(eff?.payload?.F),
+      temperature: Number(this.engine.temperature),
+    };
+    for (let i = 0; i < Math.min(SPECIES_KEYS.length, C.length); i += 1) {
+      const v = Number(C[i]);
+      if (Number.isFinite(v)) out[SPECIES_KEYS[i]] = v;
     }
+    return out;
   }
 
-  /**
-   * Create central finite difference second derivative operator.
-   * @returns {Array} - Second derivative operator matrix.
-   */
-  _makeD2operator() { // create the central second derivative operator
-    const I = math.diag(Array(this.n_x).fill(-2), 0);
-    const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]);
-    const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]);
-    const D2 = math.add(I, A, B);
-    D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
-    D2[this.n_x - 1] = Array(this.n_x).fill(0);
-    return D2;
+  getStatusBadge() {
+    const eff = this.engine.getEffluent;
+    const F = Number(eff?.payload?.F) || 0;
+    const SO = Array.isArray(eff?.payload?.C) ? Number(eff.payload.C[0]) : NaN;
+    const so = Number.isFinite(SO) ? SO.toFixed(2) : '—';
+    return statusBadge.compose(
+      [`${this.engine.constructor.name.replace('Reactor_', '')}`,
+       `T=${Number(this.engine.temperature).toFixed(1)} C`,
+       `F=${F.toFixed(2)} m³/d`,
+       `S_O=${so} mg/L`],
+      { fill: 'green', shape: 'dot' },
+    );
+  }
+
+  close() {
+    this.engine?.emitter?.removeAllListeners?.();
+    super.close();
   }
 }
 
-module.exports = { Reactor_CSTR, Reactor_PFR };
-
-// DEBUG
-// state: 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
-// let initial_state = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1];
-// const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
-// Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
-// Reactor.Fs[0] = 10;
-// Reactor.D = 0.01;
-// let N = 0;
-// while (N < 5000) {
-//     console.log(Reactor.tick(0.001));
-//     N += 1;
-// }
+module.exports = Reactor;
+module.exports.Reactor = Reactor;
+module.exports.Reactor_CSTR = Reactor_CSTR;
+module.exports.Reactor_PFR  = Reactor_PFR;
+// POSITIONS is consumed by older test setups; surface it here so they don't
+// need to chase down generalFunctions internals.
+module.exports.POSITIONS    = POSITIONS;

test/basic/constructor.basic.test.js

@@ -3,14 +3,18 @@ const assert = require('node:assert/strict');
 
 const NodeClass = require('../../src/nodeClass');
 const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
-const { makeUiConfig, makeReactorConfig, makeNodeStub } = require('../helpers/factories');
+const { makeUiConfig } = require('../helpers/factories');
 
-test('_loadConfig coerces numeric fields and builds initial state vector', () => {
+// These tests pinned the old private _loadConfig / _setupClass methods on
+// the pre-refactor nodeClass. After the BaseNodeAdapter migration the
+// same logic lives in buildDomainConfig + the Reactor wrapper's engine
+// selector. We exercise both surfaces directly.
+
+test('buildDomainConfig coerces numeric fields and builds initial state vector', () => {
   const inst = Object.create(NodeClass.prototype);
   inst.node = { id: 'n-reactor-1' };
   inst.name = 'reactor';
-
-  inst._loadConfig(
+  const dc = inst.buildDomainConfig(
     makeUiConfig({
       volume: '12.5',
       length: '9',
@@ -22,34 +26,40 @@ test('_loadConfig coerces numeric fields and builds initial state vector', () =>
     }),
   );
 
-  assert.equal(inst.config.volume, 12.5);
-  assert.equal(inst.config.length, 9);
-  assert.equal(inst.config.resolution_L, 7);
-  assert.equal(inst.config.alpha, 0.5);
-  assert.equal(inst.config.n_inlets, 3);
-  assert.equal(inst.config.timeStep, 2);
-  assert.equal(inst.config.initialState.length, 13);
-  assert.equal(inst.config.initialState[0], 1.1);
+  assert.equal(dc.reactor.volume, 12.5);
+  assert.equal(dc.reactor.length, 9);
+  assert.equal(dc.reactor.resolution_L, 7);
+  assert.equal(dc.reactor.alpha, 0.5);
+  assert.equal(dc.reactor.n_inlets, 3);
+  assert.equal(dc.reactor.timeStep, 2);
+  assert.equal(Object.keys(dc.initialState).length, 13);
+  assert.equal(dc.initialState.S_O, 1.1);
 });
 
-test('_setupClass selects Reactor_CSTR when configured as CSTR', () => {
-  const inst = Object.create(NodeClass.prototype);
-  inst.node = makeNodeStub();
-  inst.config = makeReactorConfig({ reactor_type: 'CSTR' });
-
-  inst._setupClass();
-
-  assert.ok(inst.source instanceof Reactor_CSTR);
-  assert.equal(inst.node.source, inst.source);
+test('Reactor wrapper instantiates CSTR engine when configured as CSTR', () => {
+  const Reactor = require('../../src/specificClass');
+  const config = {
+    general: { name: 'reactor', id: 'n', logging: { enabled: false, logLevel: 'error' } },
+    functionality: { softwareType: 'reactor', positionVsParent: 'atEquipment' },
+    reactor: { reactor_type: 'CSTR', volume: 100, length: 10, resolution_L: 5, alpha: 0,
+               n_inlets: 1, kla: NaN, timeStep: 1 },
+    initialState: { S_O: 0, S_I: 30, S_S: 100, S_NH: 16, S_N2: 0, S_NO: 0, S_HCO: 5,
+                    X_I: 25, X_S: 75, X_H: 30, X_STO: 0, X_A: 0.001, X_TS: 125 },
+  };
+  const r = new Reactor(config);
+  assert.ok(r.engine instanceof Reactor_CSTR);
 });
 
-test('_setupClass selects Reactor_PFR when configured as PFR', () => {
-  const inst = Object.create(NodeClass.prototype);
-  inst.node = makeNodeStub();
-  inst.config = makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5 });
-
-  inst._setupClass();
-
-  assert.ok(inst.source instanceof Reactor_PFR);
-  assert.equal(inst.node.source, inst.source);
+test('Reactor wrapper instantiates PFR engine when configured as PFR', () => {
+  const Reactor = require('../../src/specificClass');
+  const config = {
+    general: { name: 'reactor', id: 'n', logging: { enabled: false, logLevel: 'error' } },
+    functionality: { softwareType: 'reactor', positionVsParent: 'atEquipment' },
+    reactor: { reactor_type: 'PFR', volume: 100, length: 10, resolution_L: 5, alpha: 0,
+               n_inlets: 1, kla: NaN, timeStep: 1 },
+    initialState: { S_O: 0, S_I: 30, S_S: 100, S_NH: 16, S_N2: 0, S_NO: 0, S_HCO: 5,
+                    X_I: 25, X_S: 75, X_H: 30, X_STO: 0, X_A: 0.001, X_TS: 125 },
+  };
+  const r = new Reactor(config);
+  assert.ok(r.engine instanceof Reactor_PFR);
 });

test/basic/input-routing.basic.test.js

@@ -2,72 +2,51 @@ const test = require('node:test');
 const assert = require('node:assert/strict');
 
 const NodeClass = require('../../src/nodeClass');
+const commands = require('../../src/commands');
+const { createRegistry } = require('generalFunctions');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 
-test('_attachInputHandler routes supported topics to source methods/setters', () => {
+// Post-refactor: dispatch goes through the commands registry built by
+// BaseNodeAdapter (this._commands). We seed the registry on a prototype-
+// derived instance, then drive _attachInputHandler the same way the live
+// adapter would.
+
+test('input handler routes legacy topic aliases to engine setters', async () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
   const calls = [];
 
   const source = {
-    updateState(timestamp) {
-      calls.push(['clock', timestamp]);
-    },
+    logger: { warn: () => {}, info: () => {}, debug: () => {}, error: () => {} },
+    updateState(t) { calls.push(['clock', t]); },
     childRegistrationUtils: {
-      registerChild(childSource, position) {
-        calls.push(['registerChild', childSource, position]);
-      },
+      registerChild(childSource, position) { calls.push(['registerChild', childSource, position]); },
     },
   };
 
-  Object.defineProperty(source, 'setInfluent', {
-    set(v) {
-      calls.push(['Fluent', v]);
-    },
-  });
-
-  Object.defineProperty(source, 'setOTR', {
-    set(v) {
-      calls.push(['OTR', v]);
-    },
-  });
-
-  Object.defineProperty(source, 'setTemperature', {
-    set(v) {
-      calls.push(['Temperature', v]);
-    },
-  });
-
-  Object.defineProperty(source, 'setDispersion', {
-    set(v) {
-      calls.push(['Dispersion', v]);
-    },
-  });
+  Object.defineProperty(source, 'setInfluent',    { set(v) { calls.push(['Fluent',      v]); } });
+  Object.defineProperty(source, 'setOTR',         { set(v) { calls.push(['OTR',         v]); } });
+  Object.defineProperty(source, 'setTemperature', { set(v) { calls.push(['Temperature', v]); } });
+  Object.defineProperty(source, 'setDispersion',  { set(v) { calls.push(['Dispersion',  v]); } });
 
   inst.node = node;
-  inst.RED = makeREDStub({
-    childA: {
-      source: { id: 'child-source-A' },
-    },
-  });
+  inst.RED = makeREDStub({ childA: { source: { id: 'child-source-A' } } });
   inst.source = source;
-
+  inst._commands = createRegistry(commands, { logger: source.logger });
   inst._attachInputHandler();
 
   const onInput = node._handlers.input;
-  const sent = [];
   let doneCount = 0;
+  const done = () => { doneCount += 1; };
 
-  onInput({ topic: 'clock', timestamp: 1000 }, (msg) => sent.push(msg), () => doneCount++);
-  onInput({ topic: 'Fluent', payload: { inlet: 0, F: 10, C: [] } }, () => {}, () => doneCount++);
-  onInput({ topic: 'OTR', payload: 3.5 }, () => {}, () => doneCount++);
-  onInput({ topic: 'Temperature', payload: 18.2 }, () => {}, () => doneCount++);
-  onInput({ topic: 'Dispersion', payload: 0.2 }, () => {}, () => doneCount++);
-  onInput({ topic: 'registerChild', payload: 'childA', positionVsParent: 'upstream' }, () => {}, () => doneCount++);
+  await onInput({ topic: 'clock', timestamp: 1000 }, () => {}, done);
+  await onInput({ topic: 'Fluent', payload: { inlet: 0, F: 10, C: [] } }, () => {}, done);
+  await onInput({ topic: 'OTR', payload: 3.5 }, () => {}, done);
+  await onInput({ topic: 'Temperature', payload: 18.2 }, () => {}, done);
+  await onInput({ topic: 'Dispersion', payload: 0.2 }, () => {}, done);
+  await onInput({ topic: 'registerChild', payload: 'childA', positionVsParent: 'upstream' }, () => {}, done);
 
   assert.equal(doneCount, 6);
-  assert.equal(sent.length, 1);
-  assert.equal(Array.isArray(sent[0]), true);
   assert.deepEqual(calls[0], ['clock', 1000]);
   assert.equal(calls.some((x) => x[0] === 'Fluent'), true);
   assert.equal(calls.some((x) => x[0] === 'OTR'), true);

test/basic/register-child.basic.test.js

@@ -4,28 +4,21 @@ const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub } = require('../helpers/factories');
 
-test('_registerChild emits delayed registration message on output 2', () => {
+// Post-refactor: BaseNodeAdapter handles registration via _scheduleRegistration
+// (was _registerChild). Topic moved from 'registerChild' to 'child.register'.
+test('_scheduleRegistration emits delayed child.register message on output 2', () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
 
   inst.node = node;
-  inst.config = {
-    functionality: {
-      positionVsParent: 'downstream',
-    },
-  };
+  inst.config = { functionality: { positionVsParent: 'downstream', distance: null } };
 
   const originalSetTimeout = global.setTimeout;
   const delays = [];
-
-  global.setTimeout = (fn, ms) => {
-    delays.push(ms);
-    fn();
-    return 1;
-  };
+  global.setTimeout = (fn, ms) => { delays.push(ms); fn(); return 1; };
 
   try {
-    inst._registerChild();
+    inst._scheduleRegistration();
   } finally {
     global.setTimeout = originalSetTimeout;
   }
@@ -33,7 +26,7 @@ test('_registerChild emits delayed registration message on output 2', () => {
   assert.deepEqual(delays, [100]);
   assert.equal(node._sent.length, 1);
   assert.equal(Array.isArray(node._sent[0]), true);
-  assert.equal(node._sent[0][2].topic, 'registerChild');
+  assert.equal(node._sent[0][2].topic, 'child.register');
   assert.equal(node._sent[0][2].payload, node.id);
   assert.equal(node._sent[0][2].positionVsParent, 'downstream');
 });

test/basic/speedup-factor.basic.test.js

@@ -2,8 +2,8 @@ const test = require('node:test');
 const assert = require('node:assert/strict');
 
 const { Reactor_CSTR } = require('../../src/specificClass');
-const nodeClass = require('../../src/nodeClass');
-const { makeReactorConfig, makeUiConfig, makeNodeStub, makeREDStub } = require('../helpers/factories');
+const NodeClass = require('../../src/nodeClass');
+const { makeReactorConfig, makeUiConfig } = require('../helpers/factories');
 
 /**
  * Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
@@ -29,25 +29,22 @@ test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () =
   assert.equal(reactor.speedUpFactor, 60, 'speedUpFactor=60 should be accepted');
 });
 
-test('nodeClass passes speedUpFactor from uiConfig to reactor config', () => {
-  const uiConfig = makeUiConfig({ speedUpFactor: 5 });
-  const node = makeNodeStub();
-  const RED = makeREDStub();
-
-  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
-  assert.equal(nc.source.speedUpFactor, 5, 'nodeClass should pass speedUpFactor=5 to specificClass');
+test('buildDomainConfig propagates speedUpFactor from uiConfig', () => {
+  const inst = Object.create(NodeClass.prototype);
+  inst.node = { id: 'n-reactor' };
+  inst.name = 'reactor';
+  const dc = inst.buildDomainConfig(makeUiConfig({ speedUpFactor: 5 }));
+  assert.equal(dc.reactor.speedUpFactor, 5);
 });
 
-test('nodeClass defaults speedUpFactor to 1 when not in uiConfig', () => {
-  const uiConfig = makeUiConfig();
-  // Ensure speedUpFactor is not set
-  delete uiConfig.speedUpFactor;
-
-  const node = makeNodeStub();
-  const RED = makeREDStub();
-
-  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
-  assert.equal(nc.source.speedUpFactor, 1, 'nodeClass should default speedUpFactor to 1');
+test('buildDomainConfig defaults speedUpFactor to 1 when missing from uiConfig', () => {
+  const inst = Object.create(NodeClass.prototype);
+  inst.node = { id: 'n-reactor' };
+  inst.name = 'reactor';
+  const ui = makeUiConfig();
+  delete ui.speedUpFactor;
+  const dc = inst.buildDomainConfig(ui);
+  assert.equal(dc.reactor.speedUpFactor, 1);
 });
 
 test('updateState with speedUpFactor=1 advances roughly real-time', () => {
@@ -56,13 +53,9 @@ test('updateState with speedUpFactor=1 advances roughly real-time', () => {
   config.n_inlets = 1;
   const reactor = new Reactor_CSTR(config);
 
-  // Set a known start time
   const t0 = reactor.currentTime;
-  // Advance by 2 seconds real time
   reactor.updateState(t0 + 2000);
 
-  // With speedUpFactor=1, simulation should have advanced ~2 seconds worth
-  // (not 120 seconds like with the old hardcoded 60x factor)
   const elapsed = reactor.currentTime - t0;
   assert.ok(elapsed < 5000, `Elapsed ${elapsed}ms should be close to 2000ms, not 120000ms (old 60x factor)`);
 });

test/edge/invalid-reactor-type.edge.test.js

@@ -1,15 +1,21 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub, makeUiConfig } = require('../helpers/factories');
+const Reactor = require('../../src/specificClass');
+const { Reactor_CSTR } = require('../../src/specificClass');
 
-test('_setupClass with unknown reactor_type throws (known error-path behavior)', () => {
-  const inst = Object.create(NodeClass.prototype);
-  inst.node = makeNodeStub();
-  inst.config = makeUiConfig({ reactor_type: 'UNKNOWN_TYPE' });
+// Post-refactor: an unknown reactor_type falls back to CSTR and warns,
+// rather than throwing.
+test('Reactor wrapper falls back to CSTR when reactor_type is unknown', () => {
+  const config = {
+    general: { name: 'reactor', id: 'n', logging: { enabled: false, logLevel: 'error' } },
+    functionality: { softwareType: 'reactor', positionVsParent: 'atEquipment' },
+    reactor: { reactor_type: 'UNKNOWN_TYPE', volume: 100, length: 10, resolution_L: 5,
+               alpha: 0, n_inlets: 1, kla: NaN, timeStep: 1 },
+    initialState: { S_O: 0, S_I: 30, S_S: 100, S_NH: 16, S_N2: 0, S_NO: 0, S_HCO: 5,
+                    X_I: 25, X_S: 75, X_H: 30, X_STO: 0, X_A: 0.001, X_TS: 125 },
+  };
 
-  assert.throws(() => {
-    inst._setupClass();
-  });
+  const r = new Reactor(config);
+  assert.ok(r.engine instanceof Reactor_CSTR);
 });

test/edge/invalid-topic.edge.test.js

@@ -2,26 +2,27 @@ const test = require('node:test');
 const assert = require('node:assert/strict');
 
 const NodeClass = require('../../src/nodeClass');
+const commands = require('../../src/commands');
+const { createRegistry } = require('generalFunctions');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 
-test('unknown input topic does not throw and still calls done', () => {
+test('unknown input topic does not throw and still calls done', async () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
 
   inst.node = node;
   inst.RED = makeREDStub();
   inst.source = {
-    childRegistrationUtils: {
-      registerChild() {},
-    },
+    logger: { warn: () => {}, info: () => {}, debug: () => {}, error: () => {} },
+    childRegistrationUtils: { registerChild() {} },
     updateState() {},
   };
-
+  inst._commands = createRegistry(commands, { logger: inst.source.logger });
   inst._attachInputHandler();
 
   let doneCalled = 0;
-  assert.doesNotThrow(() => {
-    node._handlers.input({ topic: 'somethingUnknown', payload: 1 }, () => {}, () => {
+  await assert.doesNotReject(async () => {
+    await node._handlers.input({ topic: 'somethingUnknown', payload: 1 }, () => {}, () => {
       doneCalled += 1;
     });
   });

test/edge/missing-child.edge.test.js

@@ -2,24 +2,25 @@ const test = require('node:test');
 const assert = require('node:assert/strict');
 
 const NodeClass = require('../../src/nodeClass');
+const commands = require('../../src/commands');
+const { createRegistry } = require('generalFunctions');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 
-test('registerChild with unknown node id is ignored without throwing', () => {
+test('registerChild with unknown node id is ignored without throwing', async () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
 
   inst.node = node;
   inst.RED = makeREDStub();
   inst.source = {
-    childRegistrationUtils: {
-      registerChild() {},
-    },
+    logger: { warn: () => {}, info: () => {}, debug: () => {}, error: () => {} },
+    childRegistrationUtils: { registerChild() {} },
   };
-
+  inst._commands = createRegistry(commands, { logger: inst.source.logger });
   inst._attachInputHandler();
 
-  assert.doesNotThrow(() => {
-    node._handlers.input(
+  await assert.doesNotReject(async () => {
+    await node._handlers.input(
       { topic: 'registerChild', payload: 'missing-child', positionVsParent: 'upstream' },
       () => {},
       () => {},

test/integration/tick-loop.integration.test.js

@@ -4,19 +4,27 @@ const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub } = require('../helpers/factories');
 
-test('_tick emits source effluent on process output', () => {
+// Post-refactor: BaseNodeAdapter drives tick + status loops. The reactor
+// nodeClass overrides _emitOutputs to preserve the Fluent / GridProfile
+// Port-0 contract (delta-compressed payloads can't carry the C-vector).
+
+test('_emitOutputs emits effluent on process output', () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
 
   inst.node = node;
+  inst.config = { functionality: { softwareType: 'reactor' }, general: { id: 'r-1' } };
   inst._output = { formatMsg() { return null; } };
   inst.source = {
-    get getEffluent() {
-      return { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 };
-    },
+    engine: { temperature: 18, getEffluent: { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 }, get getGridProfile() { return null; } },
+    config: inst.config,
+    updateState() {},
+    get getEffluent()    { return this.engine.getEffluent; },
+    get getGridProfile() { return this.engine.getGridProfile; },
+    getOutput() { return {}; },
   };
 
-  inst._tick();
+  inst._emitOutputs();
 
   assert.equal(node._sent.length, 1);
   assert.equal(node._sent[0][0].topic, 'Fluent');
@@ -24,7 +32,7 @@ test('_tick emits source effluent on process output', () => {
   assert.equal(node._sent[0][2], null);
 });
 
-test('_tick emits reactor telemetry on influx output', () => {
+test('_emitOutputs emits reactor telemetry on influx output', () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
   let captured = null;
@@ -32,30 +40,28 @@ test('_tick emits reactor telemetry on influx output', () => {
   inst.node = node;
   inst.config = { functionality: { softwareType: 'reactor' }, general: { id: 'reactor-node-1' } };
   inst._output = {
-    formatMsg(output, config, format) {
-      captured = { output, config, format };
-      return { topic: 'reactor_reactor-node-1', payload: { measurement: 'reactor_reactor-node-1', fields: output } };
-    }
-  };
-  inst.source = {
-    temperature: 19.5,
-    get getGridProfile() {
-      return null;
+    formatMsg(output, _config, format) {
+      captured = { output, format };
+      return { topic: `reactor_${inst.config.general.id}`, payload: { measurement: 'reactor', fields: output } };
     },
-    get getEffluent() {
-      return {
-        topic: 'Fluent',
-        payload: {
-          inlet: 0,
-          F: 42,
-          C: [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500]
-        },
-        timestamp: 1
-      };
+  };
+  const effluent = { topic: 'Fluent', payload: { inlet: 0, F: 42, C: [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500] }, timestamp: 1 };
+  inst.source = {
+    engine: { temperature: 19.5, getEffluent: effluent, get getGridProfile() { return null; } },
+    config: inst.config,
+    updateState() {},
+    get getEffluent()    { return this.engine.getEffluent; },
+    get getGridProfile() { return this.engine.getGridProfile; },
+    getOutput() {
+      const C = effluent.payload.C;
+      const out = { flow_total: effluent.payload.F, temperature: 19.5 };
+      const keys = ['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'];
+      for (let i = 0; i < keys.length; i += 1) out[keys[i]] = C[i];
+      return out;
     },
   };
 
-  inst._tick();
+  inst._emitOutputs();
 
   assert.equal(node._sent.length, 1);
   assert.equal(node._sent[0][0].topic, 'Fluent');
@@ -68,67 +74,30 @@ test('_tick emits reactor telemetry on influx output', () => {
   assert.equal(captured.output.X_TS, 2500);
 });
 
-test('_startTickLoop schedules periodic tick after startup delay', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const delays = [];
-  const intervals = [];
-  let tickCount = 0;
-
-  inst._tick = () => {
-    tickCount += 1;
-  };
-
-  const originalSetTimeout = global.setTimeout;
-  const originalSetInterval = global.setInterval;
-
-  global.setTimeout = (fn, ms) => {
-    delays.push(ms);
-    fn();
-    return 10;
-  };
-
-  global.setInterval = (fn, ms) => {
-    intervals.push(ms);
-    fn();
-    return 22;
-  };
-
-  try {
-    inst._startTickLoop();
-  } finally {
-    global.setTimeout = originalSetTimeout;
-    global.setInterval = originalSetInterval;
-  }
-
-  assert.deepEqual(delays, [1000]);
-  assert.deepEqual(intervals, [1000]);
-  assert.equal(inst._tickInterval, 22);
-  assert.equal(tickCount, 1);
-});
-
-test('_attachCloseHandler clears tick interval and calls done callback', () => {
+test('_emitOutputs also emits GridProfile when engine exposes one', () => {
   const inst = Object.create(NodeClass.prototype);
   const node = makeNodeStub();
-  inst.node = node;
-  inst._tickInterval = 55;
 
-  const cleared = [];
-  const originalClearInterval = global.clearInterval;
-  global.clearInterval = (id) => {
-    cleared.push(id);
+  inst.node = node;
+  inst.config = { functionality: { softwareType: 'reactor' }, general: { id: 'r-1' } };
+  inst._output = { formatMsg() { return null; } };
+  const grid = { grid: [[0]], n_x: 1, d_x: 1, length: 1, species: [], timestamp: 1 };
+  inst.source = {
+    engine: {
+      temperature: 18,
+      getEffluent: { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 },
+      get getGridProfile() { return grid; },
+    },
+    config: inst.config,
+    updateState() {},
+    get getEffluent()    { return this.engine.getEffluent; },
+    get getGridProfile() { return this.engine.getGridProfile; },
+    getOutput() { return {}; },
   };
 
-  let doneCalled = 0;
+  inst._emitOutputs();
 
-  try {
-    inst._attachCloseHandler();
-    node._handlers.close(() => {
-      doneCalled += 1;
-    });
-  } finally {
-    global.clearInterval = originalClearInterval;
-  }
-
-  assert.deepEqual(cleared, [55]);
-  assert.equal(doneCalled, 1);
+  assert.equal(node._sent.length, 2);
+  assert.equal(node._sent[0][0].topic, 'GridProfile');
+  assert.equal(node._sent[1][0].topic, 'Fluent');
 });

wiki/Home.md

@@ -0,0 +1,285 @@
+# reactor
+
+> **Reflects code as of `b8247fc` · regenerated `2026-05-11` via `npm run wiki:all`**
+> If this banner is stale, the page may be out of date. Treat as informative, not authoritative.
+
+## 1. What this node is
+
+**reactor** is an S88 Unit that wraps an ASM3 biological-process engine — either a CSTR (fully mixed tank) or a PFR (plug-flow with axial dispersion). It integrates 13 species (S_O, S_NH, X_H, X_TS, …) and emits the effluent vector each tick. Drives a settler downstream and accepts a recirculation pump child.
+
+## 2. Position in the platform
+
+```mermaid
+flowchart LR
+    upstream[reactor<br/>upstream<br/>Unit]:::unit
+    reactor[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
+
+    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`.
+
+## 3. Capability matrix
+
+| Capability | Status | Notes |
+|---|---|---|
+| ASM3 13-species ODE integration | ✅ | CSTR + PFR engines under `kinetics/`. |
+| CSTR (fully mixed) | ✅ | Single concentration vector per tick. |
+| PFR (axial discretization) | ✅ | `resolution_L` grid cells; emits `GridProfile` alongside `Fluent`. |
+| Multi-inlet mixing | ✅ | `n_inlets`; each inlet receives its own `data.fluent` with `inlet` index. |
+| Temperature reconcile from measurement | ✅ | `temperature.measured.atEquipment` writes `engine.temperature`. |
+| Oxygen reconcile (PFR) | ✅ | `quantity (oxygen).measured.<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/>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
+```
+
+| 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 | Effect |
+|---|---|---|---|
+| `data.clock` | `clock` | `any` | Pushes a value into the node's measurement stream. |
+| `data.fluent` | `Fluent` | `object` | Pushes a value into the node's measurement stream. |
+| `data.otr` | `OTR` | `any` | Pushes a value into the node's measurement stream. |
+| `data.temperature` | `Temperature` | `any` | Pushes a value into the node's measurement stream. |
+| `data.dispersion` | `Dispersion` | `any` | Pushes a value into the node's measurement stream. |
+| `child.register` | `registerChild` | `any` | Parent/child plumbing — registers or unregisters a child node. |
+
+<!-- END AUTOGEN: topic-contract -->
+
+## 6. Child registration
+
+```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. |
+
+## 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):
+
+```json
+{
+  "flow_total": 1000,
+  "temperature": 15.2,
+  "S_O": 2.1,
+  "S_I": 30,
+  "S_S": 12.4,
+  "S_NH": 0.8,
+  "S_N2": 4.3,
+  "S_NO": 18.6,
+  "S_HCO": 4.2,
+  "X_I": 1050,
+  "X_S": 65,
+  "X_H": 2150,
+  "X_STO": 4.5,
+  "X_A": 215,
+  "X_TS": 3680
+}
+```
+
+Species ordering follows ASM3: indices 0–6 are soluble, 7–12 are particulate. `flow_total` is the effluent flow (m³/d); the reactor uses days as the time unit internally.
+
+## 9. Configuration — editor form ↔ config keys
+
+```mermaid
+flowchart TB
+    subgraph editor["Node-RED editor form"]
+        f1[Reactor type CSTR / PFR]
+        f2[Volume m3]
+        f3[Length m + resolution]
+        f4[Alpha dispersion]
+        f5[KLa 1/h]
+        f6[Time step + speed-up]
+        f7[Initial state 13 species]
+    end
+    subgraph config["Domain config slice"]
+        c1[reactor.reactor_type]
+        c2[reactor.volume]
+        c3[reactor.length<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
+```
+
+| Form field | Config key | Default | Range | Where used |
+|---|---|---|---|---|
+| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` | engine selection in `_buildEngine` |
+| Volume (m³) | `reactor.volume` | `1000` | > 0 | residence time, mass balance |
+| Length (m) | `reactor.length` | `10` | > 0 | PFR only — axial extent |
+| Resolution L | `reactor.resolution_L` | `10` | ≥ 1 | PFR grid cell count |
+| Alpha | `reactor.alpha` | `0.5` | 0–1 | dispersion vs plug-flow blend |
+| Inlets | `reactor.n_inlets` | `1` | ≥ 1 | `Fs[]` / `Cs_in[]` array sizes |
+| KLa (1/h) | `reactor.kla` | `0` | ≥ 0 | aeration mass transfer (NaN → use `data.otr`) |
+| Time step (h) | `reactor.timeStep` | `0.001` | ≥ 0.0001 | integrator inner step |
+| Speed-up factor | `reactor.speedUpFactor` | `1` | ≥ 1 | wall-clock → process-time multiplier |
+| Initial S_NH | `initialState.S_NH` | `25` | ≥ 0 (mg/L) | starting ammonium |
+| Initial X_H | `initialState.X_H` | `2000` | ≥ 0 (mg/L) | starting heterotroph biomass |
+| Initial X_A | `initialState.X_A` | `200` | ≥ 0 (mg/L) | starting autotroph biomass — must be ≥ ~50 for nitrification |
+| Initial X_TS | `initialState.X_TS` | `3500` | ≥ 0 (mg/L) | starting TSS — drives settler split |
+
+## 10. State chart
+
+Skipped — reactor has no FSM. It runs continuous-state ODE integration; the engine's only stateful event is `stateChange`, fired after every successful integration advance. See section 7 for the integration sequence.
+
+## 11. Examples
+
+| Tier | File | What it shows | Status |
+|---|---|---|---|
+| Basic | `examples/basic.flow.json` | CSTR with one inlet, watch `Fluent` effluent | ✅ in repo |
+| Integration | `examples/integration.flow.json` | upstream reactor → reactor → settler chain | ✅ in repo |
+| Edge | `examples/edge.flow.json` | PFR with dispersion + multi-inlet | ✅ in repo |
+| Companions | `additional_nodes/*` | recirculation-pump + settling-basin Node-RED nodes shipped from this repo | ✅ in repo |
+
+One screenshot per tier where helpful. PNG ≤ 200 KB under `wiki/_partial-screenshots/reactor/`.
+
+## 12. Debug recipes
+
+| Symptom | First thing to check | Where to look |
+|---|---|---|
+| Nitrification doesn't proceed (S_NH stays high) | `initialState.X_A` must be ≥ ~50 mg/L. Defaulting to `0.001` (a known footgun) means no autotrophs. | `generalFunctions/src/configs/reactor.json` |
+| `Fluent` effluent flow zero | No `data.clock` ticks arriving, or `data.fluent` never set `Fs[0] > 0`. | `commands/handlers.js`, engine `setInfluent` |
+| PFR `GridProfile` not emitted | `reactor_type` set to `CSTR` — only PFR emits grid. | `_buildEngine` switch |
+| Settler downstream not updating | `stateChange` event listener path: settler must subscribe to `reactor.emitter`, NOT `reactor.measurements.emitter`. | settler `_connectReactor` |
+| Temperature reconcile silently ignored | Child measurement's `asset.type` not `temperature` exactly, or `positionVsParent` not `atEquipment`. | `engine._connectMeasurement` |
+| Integrator slow / stalls | `reactor.timeStep` too small for `speedUpFactor`. Internal `n_iter` count blows up. | `engine.updateState` |
+| `wiki:datamodel` script slow / hangs | `mathjs` cold-start ~13 s; instantiation depends on it transitively. See known-limitations row 1. | `kinetics/baseEngine.js` |
+
+## 13. When you would NOT use this node
+
+- Use reactor for **ASM3 biological treatment** modelling (activated sludge, nitrification, denitrification). For aerobic-only or simpler kinetics, the ASM3 species vector is overkill.
+- Don't use reactor for a passive equalisation tank — the kinetics engines assume reactions are happening.
+- Skip reactor when you only need a residence-time delay; a simple buffer node is lighter and doesn't require `mathjs`.
+
+## 14. Known limitations / current issues
+
+| # | Issue | Tracked in |
+|---|---|---|
+| 1 | `mathjs` cold-start adds ~13 s to first `require()` — `wiki:datamodel` auto-gen may time out on the 60 s wrapper. Falls back to the hand-curated `concrete sample` block. | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" |
+| 2 | `initialState.X_A` default of `200` mg/L is correct; older config snapshots used `0.001` which silently disabled nitrification. Verify on every new deploy. | `generalFunctions/src/configs/reactor.json` |
+| 3 | `getEffluent` shape historically varied (array vs single envelope) — settler's `_connectReactor` tolerates both. Don't break the contract without updating settler. | `nodes/settler/src/specificClass.js → _connectReactor` |
+| 4 | `additional_nodes/recirculation-pump` and `settling-basin` are legacy companions — not yet refactored to BaseDomain. | P6.5 follow-up |
+| 5 | `reaction_modules/` is a legacy plug-in directory not consumed by the current engines. Removal pending. | P6.5 follow-up |