Expose output format selectors in editor

Unknown reactor type is a configuration error that should fail loudly.
Converted console.log to logger.warn for unknown topics.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

additional_nodes/recirculation-pump.js

@@ -3,13 +3,12 @@ module.exports = function(RED) {
         RED.nodes.createNode(this, config);
         var node = this;
 
-        let name = config.name;
         let F2 = parseFloat(config.F2);
         const inlet_F2 = parseInt(config.inlet);
 
         node.on('input', function(msg, send, done) {
             switch (msg.topic) {
-                case "Fluent":
+                case "Fluent": {
                     // conserve volume flow debit
                     let F_in = msg.payload.F;
                     let F1 = Math.max(F_in - F2, 0);
@@ -24,6 +23,7 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
+                }
                 case "clock":
                     break;
                 default:

additional_nodes/settling-basin.js

@@ -3,13 +3,12 @@ module.exports = function(RED) {
         RED.nodes.createNode(this, config);
         var node = this;
 
-        let name = config.name;
         let TS_set = parseFloat(config.TS_set);
         const inlet_sludge = parseInt(config.inlet);
 
         node.on('input', function(msg, send, done) {
             switch (msg.topic) {
-                case "Fluent":
+                case "Fluent": {
                     // conserve volume flow debit
                     let F_in = msg.payload.F;
                     let C_in = msg.payload.C;
@@ -41,6 +40,7 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
+                }
                 case "clock":
                     break;
                 default:

examples/README.md

@@ -1,8 +0,0 @@
-# reactor Example Flows
-
-Import-ready Node-RED examples for reactor.
-
-## Files
-- basic.flow.json
-- integration.flow.json
-- edge.flow.json

examples/basic.flow.json

@@ -1,6 +0,0 @@
-[
-  {"id":"reactor_basic_tab","type":"tab","label":"reactor basic","disabled":false,"info":"reactor basic example"},
-  {"id":"reactor_basic_node","type":"reactor","z":"reactor_basic_tab","name":"reactor basic","x":420,"y":180,"wires":[["reactor_basic_dbg"]]},
-  {"id":"reactor_basic_inj","type":"inject","z":"reactor_basic_tab","name":"basic trigger","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"ping","payload":"1","payloadType":"str","x":160,"y":180,"wires":[["reactor_basic_node"]]},
-  {"id":"reactor_basic_dbg","type":"debug","z":"reactor_basic_tab","name":"reactor basic debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
-]

examples/edge.flow.json

@@ -1,6 +0,0 @@
-[
-  {"id":"reactor_edge_tab","type":"tab","label":"reactor edge","disabled":false,"info":"reactor edge example"},
-  {"id":"reactor_edge_node","type":"reactor","z":"reactor_edge_tab","name":"reactor edge","x":420,"y":180,"wires":[["reactor_edge_dbg"]]},
-  {"id":"reactor_edge_inj","type":"inject","z":"reactor_edge_tab","name":"unknown topic","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"doesNotExist","payload":"x","payloadType":"str","x":170,"y":180,"wires":[["reactor_edge_node"]]},
-  {"id":"reactor_edge_dbg","type":"debug","z":"reactor_edge_tab","name":"reactor edge debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
-]

examples/integration.flow.json

@@ -1,6 +0,0 @@
-[
-  {"id":"reactor_int_tab","type":"tab","label":"reactor integration","disabled":false,"info":"reactor integration example"},
-  {"id":"reactor_int_node","type":"reactor","z":"reactor_int_tab","name":"reactor integration","x":420,"y":180,"wires":[["reactor_int_dbg"]]},
-  {"id":"reactor_int_inj","type":"inject","z":"reactor_int_tab","name":"registerChild","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"registerChild","payload":"example-child-id","payloadType":"str","x":170,"y":180,"wires":[["reactor_int_node"]]},
-  {"id":"reactor_int_dbg","type":"debug","z":"reactor_int_tab","name":"reactor integration debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":680,"y":180,"wires":[]}
-]

package.json

@@ -17,7 +17,7 @@
   "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 reactor.js"
   },
   "node-red": {
     "nodes": {

reactor.html

@@ -1,19 +1,9 @@
-<!--
-| S88-niveau             | Primair (blokkleur) | Tekstkleur |
-| ---------------------- | ------------------- | ---------- |
-| **Area**               | `#0f52a5`           | wit        |
-| **Process Cell**       | `#0c99d9`           | wit        |
-| **Unit**               | `#50a8d9`           | zwart      |
-| **Equipment (Module)** | `#86bbdd`           | zwart      |
-| **Control Module**     | `#a9daee`           | zwart      |
-
--->
 <script src="/reactor/menu.js"></script>
 
 <script type="text/javascript">
     RED.nodes.registerType("reactor", {
-        category: "EVOLV",
+        category: "WWTP",
-        color: "#50a8d9",
+        color: "#c4cce0",
         defaults: {
             name: { value: "" },
             reactor_type: { value: "CSTR", required: true },
@@ -39,7 +29,8 @@
             X_TS_init: { value: 125.0009, required: true },
 
             timeStep: { value: 1, required: true },
-            speedUpFactor: { value: 1 },
+            processOutputFormat: { value: "process" },
+            dbaseOutputFormat: { value: "influxdb" },
 
             enableLog: { value: false },
             logLevel: { value: "error" },
@@ -50,7 +41,7 @@
         outputs: 3,
         inputLabels: ["input"],
         outputLabels: ["process", "dbase", "parent"],
-        icon: "font-awesome/fa-flask",
+        icon: "font-awesome/fa-recycle",
         label: function() {
             return this.name || "Reactor";
         },
@@ -116,10 +107,6 @@
                 type:"num",
                 types:["num"]
             })
-            $("#node-input-speedUpFactor").typedInput({
-                type:"num",
-                types:["num"]
-            })
             // Set initial visibility on dialog open
             const initialType = $("#node-input-reactor_type").typedInput("value");
             if (initialType === "CSTR") {
@@ -135,8 +122,8 @@
             }
 
             // save position field
-            if (window.EVOLV?.nodes?.reactor?.positionMenu?.saveEditor) {
+            if (window.EVOLV?.nodes?.measurement?.positionMenu?.saveEditor) {
-                window.EVOLV.nodes.reactor.positionMenu.saveEditor(this);
+                window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
             }
 
             let volume = parseFloat($("#node-input-volume").typedInput("value"));
@@ -248,9 +235,22 @@
         <label for="node-input-timeStep"><i class="fa fa-tag"></i> Time step [s]</label>
         <input type="text" id="node-input-timeStep" placeholder="s">
     </div>
+    <h3>Output Formats</h3>
     <div class="form-row">
-        <label for="node-input-speedUpFactor"><i class="fa fa-tag"></i> Speed-up factor</label>
+        <label for="node-input-processOutputFormat"><i class="fa fa-random"></i> Process Output</label>
-        <input type="text" id="node-input-speedUpFactor" placeholder="1 = real-time">
+        <select id="node-input-processOutputFormat" style="width:60%;">
+            <option value="process">process</option>
+            <option value="json">json</option>
+            <option value="csv">csv</option>
+        </select>
+    </div>
+    <div class="form-row">
+        <label for="node-input-dbaseOutputFormat"><i class="fa fa-database"></i> Database Output</label>
+        <select id="node-input-dbaseOutputFormat" style="width:60%;">
+            <option value="influxdb">influxdb</option>
+            <option value="json">json</option>
+            <option value="csv">csv</option>
+        </select>
     </div>
 
     <!-- Logger fields injected here -->

src/nodeClass.js

@@ -1,4 +1,5 @@
 const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
+const { configManager } = require('generalFunctions');
 
 
 class nodeClass {
@@ -30,42 +31,36 @@ class nodeClass {
      */
     _attachInputHandler() {
         this.node.on('input', (msg, send, done) => {
-            try {
+
-                switch (msg.topic) {
+            switch (msg.topic) {
-                    case "clock":
+                case "clock":
-                        this.source.updateState(msg.timestamp);
+                    this.source.updateState(msg.timestamp);
-                        send([msg, null, null]);
+                    send([msg, null, null]);
-                        break;
+                    break;
-                    case "Fluent":
+                case "Fluent":
-                        this.source.setInfluent = msg;
+                    this.source.setInfluent = msg;
-                        break;
+                    break;
-                    case "OTR":
+                case "OTR":
-                        this.source.setOTR = msg;
+                    this.source.setOTR = msg;
-                        break;
+                    break;
-                    case "Temperature":
+                case "Temperature":
-                        this.source.setTemperature = msg;
+                    this.source.setTemperature = msg;
-                        break;
+                    break;
-                    case "Dispersion":
+                case "Dispersion":
-                        this.source.setDispersion = msg;
+                    this.source.setDispersion = msg;
-                        break;
+                    break;
-                    case 'registerChild': {
+                case 'registerChild': {
-                        const childId = msg.payload;
+                    // Register this node as a parent of the child node
-                        const childObj = this.RED.nodes.getNode(childId);
+                    const childId = msg.payload;
-                        if (!childObj || !childObj.source) {
+                    const childObj = this.RED.nodes.getNode(childId);
-                            this.source?.logger?.warn(`registerChild skipped: missing child/source for id=${childId}`);
+                    this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
-                            break;
+                    break;
-                        }
-                        this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
-                        break;
-                    }
-                    default:
-                        this.source?.logger?.warn(`Unknown topic: ${msg.topic}`);
                 }
-            } catch (error) {
+                default:
-                this.source?.logger?.error(`Input handler failure: ${error.message}`);
+                    this.source.logger.warn(`Unknown topic: ${msg.topic}`);
             }
 
-            if (typeof done === 'function') {
+            if (done) {
                 done();
             }
         });
@@ -76,20 +71,10 @@ class nodeClass {
      * @param {object} uiConfig Config set in UI in node-red
      */
     _loadConfig(uiConfig) {
-        this.config = {
+        const cfgMgr = new configManager();
-            general: {
+
-                name: uiConfig.name || this.name,
+        // Build config: base sections + reactor-specific domain config
-                id: this.node.id,
+        this.config = cfgMgr.buildConfig('reactor', uiConfig, this.node.id, {
-                unit: null,
-                logging: {
-                    enabled: uiConfig.enableLog,
-                    logLevel: uiConfig.logLevel
-                }
-            },
-            functionality: {
-                positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
-                softwareType: "reactor" // should be set in config manager
-            },
             reactor_type: uiConfig.reactor_type,
             volume: parseFloat(uiConfig.volume),
             length: parseFloat(uiConfig.length),
@@ -112,9 +97,8 @@ class nodeClass {
                 parseFloat(uiConfig.X_A_init),
                 parseFloat(uiConfig.X_TS_init)
             ],
-            timeStep: parseFloat(uiConfig.timeStep),
+            timeStep: parseFloat(uiConfig.timeStep)
-            speedUpFactor: Number(uiConfig.speedUpFactor) || 1
+        });
-        }
     }
 
     /**
@@ -145,8 +129,7 @@ class nodeClass {
                 new_reactor = new Reactor_PFR(this.config);
                 break;
             default:
-                this.node.warn("Unknown reactor type: " + this.config.reactor_type + ". Falling back to CSTR.");
+                throw new Error(`Unknown reactor type: ${this.config.reactor_type}`);
-                new_reactor = new Reactor_CSTR(this.config);
         }
 
         this.source = new_reactor; // protect from reassignment
@@ -160,19 +143,15 @@ class nodeClass {
     }
 
     _tick(){
-        const gridProfile = this.source.getGridProfile;
-        if (gridProfile) {
-            this.node.send([{ topic: "GridProfile", payload: gridProfile }, null, null]);
-        }
         this.node.send([this.source.getEffluent, null, null]);
     }
 
     _attachCloseHandler() {
         this.node.on('close', (done) => {
             clearInterval(this._tickInterval);
-            if (typeof done === 'function') done();
+            done();
         });
     }
 }
 
-module.exports = nodeClass;
+module.exports = nodeClass;

src/reaction_modules/asm3_class Koch.js

@@ -19,7 +19,7 @@ class ASM3 {
       nu_NO:    0.5,  // anoxic reduction factor        [-]
       K_O:      0.2,  // saturation constant S_0        [g O2 m-3]
       K_NO:     0.5,  // saturation constant S_NO       [g NO3-N m-3]
-      K_S:      10.,  // saturation constant S_s        [g COD m-3]
+      K_S:      10.0, // saturation constant S_s        [g COD m-3]
       K_STO:    0.1,  // saturation constant X_STO      [g X_STO g-1 X_H]
       mu_H_max: 3.,   // maximum specific growth rate   [d-1]
       K_NH:     0.01, // saturation constant S_NH3      [g NH3-N m-3]
@@ -171,7 +171,7 @@ class ASM3 {
   compute_rates(state, T = 20) {
     // 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
     const rates = Array(12);
-    const [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] = state;
+    const [S_O, , S_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 

src/reaction_modules/asm3_class.js

@@ -171,7 +171,7 @@ class ASM3 {
   compute_rates(state, T = 20) {
     // 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
     const rates = Array(12);
-    const [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] = state;
+    const [S_O, , S_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 

src/specificClass.js

@@ -1,7 +1,7 @@
 const ASM3 = require('./reaction_modules/asm3_class.js');
 const { create, all, isArray } = require('mathjs');
 const { assertNoNaN } = require('./utils.js');
-const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
+const { childRegistrationUtils, logger, MeasurementContainer, POSITIONS } = require('generalFunctions');
 const EventEmitter = require('events');
 
 const mathConfig = {
@@ -41,7 +41,7 @@ class Reactor {
 
     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
+    this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
   }
 
   /**
@@ -62,24 +62,6 @@ class Reactor {
     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.
@@ -91,8 +73,6 @@ class Reactor {
     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].
@@ -146,7 +126,6 @@ class Reactor {
       position = measurement.config.functionality.positionVsParent;
     }
     const measurementType = measurement.config.asset.type;
-    const key = `${measurementType}_${position}`;
     const eventName = `${measurementType}.measured.${position}`;
 
     // Register event listener for measurement updates
@@ -180,11 +159,11 @@ class Reactor {
   }
 
   
-  _updateMeasurement(measurementType, value, position, context) {
+  _updateMeasurement(measurementType, value, position, _context) {
     this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
     switch (measurementType) {
       case "temperature":
-        if (position == "atEquipment") {
+        if (position == POSITIONS.AT_EQUIPMENT) {
           this.temperature = value;
         }
         break;
@@ -277,18 +256,6 @@ class Reactor_PFR extends Reactor {
     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
-    };
-  }
-
   /**
    * Setter for axial dispersion.
    * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
@@ -352,22 +319,15 @@ class Reactor_PFR extends Reactor {
     return stateNew;
   }
 
-  _updateMeasurement(measurementType, value, position, context) {
+  _updateMeasurement(measurementType, value, position, _context) {
     switch(measurementType) {
-      case "quantity (oxygen)":
+      case "quantity (oxygen)": {
-        if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) {
+        let grid_pos = Math.round(position / this.config.length * this.n_x);
-          this.logger.warn(`Ignoring oxygen measurement update with invalid data (position=${position}, value=${value}).`);
+        this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
-          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;
+      }
       default:
-        super._updateMeasurement(measurementType, value, position, context);
+        super._updateMeasurement(measurementType, value, position, _context);
     }
   }
 
@@ -456,4 +416,4 @@ module.exports = { Reactor_CSTR, Reactor_PFR };
 // while (N < 5000) {
 //     console.log(Reactor.tick(0.001));
 //     N += 1;
-// }
+// }

test/README.md

@@ -1,12 +0,0 @@
-# reactor Test Suite Layout
-
-Required EVOLV layout:
-- basic/
-- integration/
-- edge/
-- helpers/
-
-Baseline structure tests:
-- basic/structure-module-load.basic.test.js
-- integration/structure-examples.integration.test.js
-- edge/structure-examples-node-type.edge.test.js

test/basic/constructor.basic.test.js

@@ -1,55 +0,0 @@
-const test = require('node:test');
-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');
-
-test('_loadConfig 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(
-    makeUiConfig({
-      volume: '12.5',
-      length: '9',
-      resolution_L: '7',
-      alpha: '0.5',
-      n_inlets: '3',
-      timeStep: '2',
-      S_O_init: '1.1',
-    }),
-  );
-
-  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);
-});
-
-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('_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/basic/cstr-tick.basic.test.js

@@ -1,42 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-const NUM_SPECIES = 13;
-
-test('Reactor_CSTR tick clips negative concentrations to zero', () => {
-  const reactor = new Reactor_CSTR(
-    makeReactorConfig({
-      reactor_type: 'CSTR',
-      volume: 1,
-      n_inlets: 1,
-      kla: NaN,
-      S_O_init: 0.1,
-      S_I_init: 0.1,
-      S_S_init: 0.1,
-      S_NH_init: 0.1,
-      S_N2_init: 0.1,
-      S_NO_init: 0.1,
-      S_HCO_init: 0.1,
-      X_I_init: 0.1,
-      X_S_init: 0.1,
-      X_H_init: 0.1,
-      X_STO_init: 0.1,
-      X_A_init: 0.1,
-      X_TS_init: 0.1,
-    }),
-  );
-
-  reactor.asm = {
-    compute_dC: () => Array(NUM_SPECIES).fill(0),
-  };
-  reactor.Fs[0] = 1;
-  reactor.Cs_in[0] = Array(NUM_SPECIES).fill(0);
-
-  reactor.tick(1);
-
-  assert.equal(reactor.state.every((v) => Number.isFinite(v) && v >= 0), true);
-  assert.equal(reactor.state.every((v) => v === 0), true);
-});

test/basic/effluent-shape.basic.test.js

@@ -1,38 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-test('CSTR getEffluent returns flat concentration vector', () => {
-  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
-  reactor.state = Array.from({ length: 13 }, (_, i) => i + 1);
-  reactor.Fs[0] = 5;
-
-  const effluent = reactor.getEffluent;
-
-  assert.equal(effluent.topic, 'Fluent');
-  assert.equal(effluent.payload.inlet, 0);
-  assert.equal(effluent.payload.F, 5);
-  assert.deepEqual(effluent.payload.C, reactor.state);
-});
-
-test('PFR getEffluent returns last slice concentration vector', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 4 }),
-  );
-
-  reactor.state = [
-    Array(13).fill(10),
-    Array(13).fill(20),
-    Array(13).fill(30),
-    Array(13).fill(40),
-  ];
-  reactor.Fs[0] = 7;
-
-  const effluent = reactor.getEffluent;
-
-  assert.equal(effluent.topic, 'Fluent');
-  assert.equal(effluent.payload.F, 7);
-  assert.deepEqual(effluent.payload.C, Array(13).fill(40));
-});

test/basic/grid-profile.basic.test.js

@@ -1,45 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-test('CSTR getGridProfile returns null', () => {
-  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
-  assert.equal(reactor.getGridProfile, null);
-});
-
-test('PFR getGridProfile returns state matrix with correct dimensions', () => {
-  const n_x = 8;
-  const length = 40;
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', resolution_L: n_x, length }),
-  );
-
-  const profile = reactor.getGridProfile;
-  assert.notEqual(profile, null);
-  assert.equal(profile.n_x, n_x);
-  assert.equal(profile.d_x, length / n_x);
-  assert.equal(profile.length, length);
-  assert.equal(profile.grid.length, n_x, 'grid should have n_x rows');
-  assert.equal(profile.grid[0].length, 13, 'each row should have 13 species');
-  assert.ok(Array.isArray(profile.species), 'species list should be an array');
-  assert.equal(profile.species.length, 13);
-  assert.equal(profile.species[3], 'S_NH');
-  assert.equal(typeof profile.timestamp, 'number');
-});
-
-test('PFR getGridProfile is mutation-safe', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', resolution_L: 5, length: 10 }),
-  );
-
-  const profile = reactor.getGridProfile;
-  const originalValue = reactor.state[0][3]; // S_NH at cell 0
-
-  // Mutate the returned grid
-  profile.grid[0][3] = 999;
-
-  // Reactor internal state should be unchanged
-  assert.equal(reactor.state[0][3], originalValue, 'mutating grid copy must not affect reactor state');
-});

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

@@ -1,77 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub, makeREDStub } = require('../helpers/factories');
-
-test('_attachInputHandler routes supported topics to source methods/setters', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const node = makeNodeStub();
-  const calls = [];
-
-  const source = {
-    updateState(timestamp) {
-      calls.push(['clock', timestamp]);
-    },
-    childRegistrationUtils: {
-      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]);
-    },
-  });
-
-  inst.node = node;
-  inst.RED = makeREDStub({
-    childA: {
-      source: { id: 'child-source-A' },
-    },
-  });
-  inst.source = source;
-
-  inst._attachInputHandler();
-
-  const onInput = node._handlers.input;
-  const sent = [];
-  let doneCount = 0;
-
-  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++);
-
-  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);
-  assert.equal(calls.some((x) => x[0] === 'Temperature'), true);
-  assert.equal(calls.some((x) => x[0] === 'Dispersion'), true);
-  assert.deepEqual(calls.at(-1), ['registerChild', { id: 'child-source-A' }, 'upstream']);
-});

test/basic/pfr-operators.basic.test.js

@@ -1,27 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-test('Reactor_PFR derivative operators have expected dimensions and boundary rows', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({
-      reactor_type: 'PFR',
-      length: 12,
-      resolution_L: 6,
-      volume: 60,
-      n_inlets: 1,
-    }),
-  );
-
-  assert.equal(reactor.D_op.length, reactor.n_x);
-  assert.equal(reactor.D2_op.length, reactor.n_x);
-  assert.equal(reactor.D_op.every((row) => row.length === reactor.n_x), true);
-  assert.equal(reactor.D2_op.every((row) => row.length === reactor.n_x), true);
-
-  assert.deepEqual(reactor.D_op[0], Array(reactor.n_x).fill(0));
-  assert.deepEqual(reactor.D_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
-  assert.deepEqual(reactor.D2_op[0], Array(reactor.n_x).fill(0));
-  assert.deepEqual(reactor.D2_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
-});

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

@@ -1,39 +0,0 @@
-const test = require('node:test');
-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', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const node = makeNodeStub();
-
-  inst.node = node;
-  inst.config = {
-    functionality: {
-      positionVsParent: 'downstream',
-    },
-  };
-
-  const originalSetTimeout = global.setTimeout;
-  const delays = [];
-
-  global.setTimeout = (fn, ms) => {
-    delays.push(ms);
-    fn();
-    return 1;
-  };
-
-  try {
-    inst._registerChild();
-  } finally {
-    global.setTimeout = originalSetTimeout;
-  }
-
-  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].payload, node.id);
-  assert.equal(node._sent[0][2].positionVsParent, 'downstream');
-});

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

@@ -1,68 +0,0 @@
-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');
-
-/**
- * Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
- */
-
-test('specificClass defaults speedUpFactor to 1 when not in config', () => {
-  const config = makeReactorConfig();
-  const reactor = new Reactor_CSTR(config);
-  assert.equal(reactor.speedUpFactor, 1, 'speedUpFactor should default to 1');
-});
-
-test('specificClass accepts speedUpFactor from config', () => {
-  const config = makeReactorConfig();
-  config.speedUpFactor = 10;
-  const reactor = new Reactor_CSTR(config);
-  assert.equal(reactor.speedUpFactor, 10, 'speedUpFactor should be read from config');
-});
-
-test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () => {
-  const config = makeReactorConfig();
-  config.speedUpFactor = 60;
-  const reactor = new Reactor_CSTR(config);
-  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('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('updateState with speedUpFactor=1 advances roughly real-time', () => {
-  const config = makeReactorConfig();
-  config.speedUpFactor = 1;
-  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/basic/structure-module-load.basic.test.js

@@ -1,8 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-test('reactor module load smoke', () => {
-  assert.doesNotThrow(() => {
-    require('../../reactor.js');
-  });
-});

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

@@ -1,15 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub, makeUiConfig } = require('../helpers/factories');
-
-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' });
-
-  assert.throws(() => {
-    inst._setupClass();
-  });
-});

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

@@ -1,30 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub, makeREDStub } = require('../helpers/factories');
-
-test('unknown input topic does not throw and still calls done', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const node = makeNodeStub();
-
-  inst.node = node;
-  inst.RED = makeREDStub();
-  inst.source = {
-    childRegistrationUtils: {
-      registerChild() {},
-    },
-    updateState() {},
-  };
-
-  inst._attachInputHandler();
-
-  let doneCalled = 0;
-  assert.doesNotThrow(() => {
-    node._handlers.input({ topic: 'somethingUnknown', payload: 1 }, () => {}, () => {
-      doneCalled += 1;
-    });
-  });
-
-  assert.equal(doneCalled, 1);
-});

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

@@ -1,28 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub, makeREDStub } = require('../helpers/factories');
-
-test('registerChild with unknown node id is ignored without throwing', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const node = makeNodeStub();
-
-  inst.node = node;
-  inst.RED = makeREDStub();
-  inst.source = {
-    childRegistrationUtils: {
-      registerChild() {},
-    },
-  };
-
-  inst._attachInputHandler();
-
-  assert.doesNotThrow(() => {
-    node._handlers.input(
-      { topic: 'registerChild', payload: 'missing-child', positionVsParent: 'upstream' },
-      () => {},
-      () => {},
-    );
-  });
-});

test/edge/pfr-measurement-grid.edge.test.js

@@ -1,16 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-test('oxygen measurement at exact reactor length is clamped to the last PFR grid index', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, n_inlets: 1 }),
-  );
-
-  assert.doesNotThrow(() => {
-    reactor._updateMeasurement('quantity (oxygen)', 2.5, 10, {});
-  });
-  assert.equal(reactor.state[reactor.n_x - 1][0], 2.5);
-});

test/edge/structure-examples-node-type.edge.test.js

@@ -1,11 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-const fs = require('node:fs');
-const path = require('node:path');
-
-const flow = JSON.parse(fs.readFileSync(path.resolve(__dirname, '../../examples/basic.flow.json'), 'utf8'));
-
-test('basic example includes node type reactor', () => {
-  const count = flow.filter((n) => n && n.type === 'reactor').length;
-  assert.equal(count >= 1, true);
-});

test/edge/zero-dispersion.edge.test.js

@@ -1,27 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-const DAY_MS = 1000 * 60 * 60 * 24;
-
-test('updateState warns when local Peclet number is too high at zero dispersion', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, volume: 50, n_inlets: 1 }),
-  );
-
-  const warnings = [];
-  reactor.logger.warn = (msg) => warnings.push(String(msg));
-
-  reactor.currentTime = 0;
-  reactor.timeStep = 1;
-  reactor.speedUpFactor = 1;
-  reactor.Fs[0] = 2;
-  reactor.D = 0;
-  reactor.tick = () => reactor.state;
-
-  reactor.updateState(DAY_MS);
-
-  assert.equal(warnings.some((w) => w.includes('Péclet number') || w.includes('Peclet number')), true);
-});

test/helpers/factories.js

@@ -1,149 +0,0 @@
-const EventEmitter = require('node:events');
-
-function makeUiConfig(overrides = {}) {
-  return {
-    name: 'reactor-test',
-    reactor_type: 'CSTR',
-    volume: 100,
-    length: 10,
-    resolution_L: 5,
-    alpha: 0,
-    n_inlets: 1,
-    kla: NaN,
-    S_O_init: 0,
-    S_I_init: 30,
-    S_S_init: 100,
-    S_NH_init: 16,
-    S_N2_init: 0,
-    S_NO_init: 0,
-    S_HCO_init: 5,
-    X_I_init: 25,
-    X_S_init: 75,
-    X_H_init: 30,
-    X_STO_init: 0,
-    X_A_init: 0.001,
-    X_TS_init: 125,
-    timeStep: 1,
-    enableLog: false,
-    logLevel: 'error',
-    positionVsParent: 'atEquipment',
-    ...overrides,
-  };
-}
-
-function makeReactorConfig(overrides = {}) {
-  const ui = makeUiConfig(overrides);
-  return {
-    general: {
-      id: 'reactor-node-1',
-      name: ui.name,
-      unit: null,
-      logging: {
-        enabled: ui.enableLog,
-        logLevel: ui.logLevel,
-      },
-    },
-    functionality: {
-      positionVsParent: ui.positionVsParent || 'atEquipment',
-      softwareType: 'reactor',
-    },
-    reactor_type: ui.reactor_type,
-    volume: Number(ui.volume),
-    length: Number(ui.length),
-    resolution_L: Number(ui.resolution_L),
-    alpha: Number(ui.alpha),
-    n_inlets: Number(ui.n_inlets),
-    kla: Number(ui.kla),
-    initialState: [
-      Number(ui.S_O_init),
-      Number(ui.S_I_init),
-      Number(ui.S_S_init),
-      Number(ui.S_NH_init),
-      Number(ui.S_N2_init),
-      Number(ui.S_NO_init),
-      Number(ui.S_HCO_init),
-      Number(ui.X_I_init),
-      Number(ui.X_S_init),
-      Number(ui.X_H_init),
-      Number(ui.X_STO_init),
-      Number(ui.X_A_init),
-      Number(ui.X_TS_init),
-    ],
-    timeStep: Number(ui.timeStep),
-  };
-}
-
-function makeNodeStub() {
-  const handlers = {};
-  const sent = [];
-  const warns = [];
-  const errors = [];
-  const statuses = [];
-
-  return {
-    id: 'reactor-node-1',
-    source: null,
-    on(event, cb) {
-      handlers[event] = cb;
-    },
-    send(msg) {
-      sent.push(msg);
-    },
-    warn(msg) {
-      warns.push(msg);
-    },
-    error(msg) {
-      errors.push(msg);
-    },
-    status(msg) {
-      statuses.push(msg);
-    },
-    _handlers: handlers,
-    _sent: sent,
-    _warns: warns,
-    _errors: errors,
-    _statuses: statuses,
-  };
-}
-
-function makeREDStub(nodeMap = {}) {
-  return {
-    nodes: {
-      getNode(id) {
-        return nodeMap[id] || null;
-      },
-      createNode() {},
-      registerType() {},
-    },
-    httpAdmin: {
-      get() {},
-    },
-  };
-}
-
-function makeMeasurementChild({
-  id = 'measurement-1',
-  name = 'temp-sensor-1',
-  distance = 'atEquipment',
-  positionVsParent = 'atEquipment',
-  type = 'temperature',
-} = {}) {
-  return {
-    config: {
-      general: { id, name },
-      functionality: { distance, positionVsParent, softwareType: 'measurement' },
-      asset: { type },
-    },
-    measurements: {
-      emitter: new EventEmitter(),
-    },
-  };
-}
-
-module.exports = {
-  makeUiConfig,
-  makeReactorConfig,
-  makeNodeStub,
-  makeREDStub,
-  makeMeasurementChild,
-};

test/integration/measurement-temperature.integration.test.js

@@ -1,26 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeReactorConfig, makeMeasurementChild } = require('../helpers/factories');
-
-test('measurement child temperature event updates reactor temperature', () => {
-  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
-
-  const measurement = makeMeasurementChild({
-    type: 'temperature',
-    distance: 'atEquipment',
-    positionVsParent: 'upstream',
-  });
-
-  reactor.registerChild(measurement, 'measurement');
-
-  measurement.measurements.emitter.emit('temperature.measured.atEquipment', {
-    childName: 'T-1',
-    value: 27.5,
-    unit: 'C',
-    timestamp: Date.now(),
-  });
-
-  assert.equal(reactor.temperature, 27.5);
-});

test/integration/otr-kla.integration.test.js

@@ -1,85 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-const NUM_SPECIES = 13;
-
-test('CSTR uses external OTR when kla is NaN', () => {
-  const reactor = new Reactor_CSTR(
-    makeReactorConfig({ reactor_type: 'CSTR', kla: NaN, n_inlets: 1 }),
-  );
-
-  reactor.asm = {
-    compute_dC: () => Array(NUM_SPECIES).fill(0),
-  };
-  reactor.Fs[0] = 0;
-  reactor.OTR = 4;
-  reactor.state = Array(NUM_SPECIES).fill(0);
-
-  reactor.tick(1);
-
-  assert.equal(reactor.state[0], 4);
-});
-
-test('CSTR uses kla-based oxygen transfer when kla is finite', () => {
-  const reactor = new Reactor_CSTR(
-    makeReactorConfig({ reactor_type: 'CSTR', kla: 2, n_inlets: 1 }),
-  );
-
-  reactor.asm = {
-    compute_dC: () => Array(NUM_SPECIES).fill(0),
-  };
-  reactor.Fs[0] = 0;
-  reactor.OTR = 1;
-  reactor.state = Array(NUM_SPECIES).fill(0);
-
-  const expected = reactor._calcOTR(0, reactor.temperature);
-  reactor.tick(1);
-
-  assert.ok(Math.abs(reactor.state[0] - expected) < 1e-9);
-});
-
-test('PFR uses external OTR branch when kla is NaN', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', kla: NaN, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
-  );
-
-  reactor.asm = {
-    compute_dC: () => Array(NUM_SPECIES).fill(0),
-  };
-  reactor.Fs[0] = 0;
-  reactor.D = 0;
-  reactor.OTR = 3;
-  reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
-
-  reactor.tick(1);
-
-  assert.equal(reactor.state[1][0], 4.5);
-  assert.equal(reactor.state[2][0], 4.5);
-  assert.equal(reactor.state[3][0], 4.5);
-  assert.equal(reactor.state[4][0], 4.5);
-});
-
-test('PFR uses kla-based transfer branch when kla is finite', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', kla: 1, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
-  );
-
-  reactor.asm = {
-    compute_dC: () => Array(NUM_SPECIES).fill(0),
-  };
-  reactor.Fs[0] = 0;
-  reactor.D = 0;
-  reactor.OTR = 0;
-  reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
-
-  const expected = reactor._calcOTR(0, reactor.temperature) * (reactor.n_x / (reactor.n_x - 2));
-  reactor.tick(1);
-
-  assert.ok(Math.abs(reactor.state[1][0] - expected) < 1e-9);
-  assert.ok(Math.abs(reactor.state[2][0] - expected) < 1e-9);
-  assert.ok(Math.abs(reactor.state[3][0] - expected) < 1e-9);
-  assert.ok(Math.abs(reactor.state[4][0] - expected) < 1e-9);
-});

test/integration/pfr-boundary.integration.test.js

@@ -1,35 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-test('_applyBoundaryConditions enforces Danckwerts inlet and Neumann outlet for flowing case', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50, alpha: 0.2 }),
-  );
-
-  reactor.Fs[0] = 2;
-  reactor.Cs_in[0] = Array(13).fill(9);
-  reactor.D = 1;
-
-  const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i));
-  reactor._applyBoundaryConditions(state);
-
-  assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
-  assert.equal(state[0].every((v) => Number.isFinite(v)), true);
-});
-
-test('_applyBoundaryConditions copies first interior slice when no flow is present', () => {
-  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50 }),
-  );
-
-  reactor.Fs[0] = 0;
-  const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i + 10));
-
-  reactor._applyBoundaryConditions(state);
-
-  assert.deepEqual(state[0], state[1]);
-  assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
-});

test/integration/structure-examples.integration.test.js

@@ -1,23 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-const fs = require('node:fs');
-const path = require('node:path');
-
-const dir = path.resolve(__dirname, '../../examples');
-
-function loadJson(file) {
-  return JSON.parse(fs.readFileSync(path.join(dir, file), 'utf8'));
-}
-
-test('examples package exists for reactor', () => {
-  for (const file of ['README.md', 'basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
-    assert.equal(fs.existsSync(path.join(dir, file)), true, file + ' missing');
-  }
-});
-
-test('example flows are parseable arrays for reactor', () => {
-  for (const file of ['basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
-    const parsed = loadJson(file);
-    assert.equal(Array.isArray(parsed), true);
-  }
-});

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

@@ -1,89 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const NodeClass = require('../../src/nodeClass');
-const { makeNodeStub } = require('../helpers/factories');
-
-test('_tick emits source effluent on process output', () => {
-  const inst = Object.create(NodeClass.prototype);
-  const node = makeNodeStub();
-
-  inst.node = node;
-  inst.source = {
-    get getEffluent() {
-      return { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 };
-    },
-  };
-
-  inst._tick();
-
-  assert.equal(node._sent.length, 1);
-  assert.equal(node._sent[0][0].topic, 'Fluent');
-  assert.equal(node._sent[0][1], null);
-  assert.equal(node._sent[0][2], null);
-});
-
-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', () => {
-  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);
-  };
-
-  let doneCalled = 0;
-
-  try {
-    inst._attachCloseHandler();
-    node._handlers.close(() => {
-      doneCalled += 1;
-    });
-  } finally {
-    global.clearInterval = originalClearInterval;
-  }
-
-  assert.deepEqual(cleared, [55]);
-  assert.equal(doneCalled, 1);
-});

test/integration/upstream-reactor.integration.test.js

@@ -1,48 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-const DAY_MS = 1000 * 60 * 60 * 24;
-
-test('registering upstream reactor subscribes to upstream stateChange events', () => {
-  const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
-  const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
-
-  let calledWith = null;
-  downstream.updateState = (timestamp) => {
-    calledWith = timestamp;
-  };
-
-  downstream.registerChild(upstream, 'reactor');
-  upstream.emitter.emit('stateChange', 12345);
-
-  assert.equal(downstream.upstreamReactor, upstream);
-  assert.equal(calledWith, 12345);
-});
-
-test('updateState pulls influent from upstream reactor effluent when linked', () => {
-  const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1, timeStep: 1 }));
-  const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
-
-  upstream.Fs[0] = 3;
-  upstream.state = Array(13).fill(11);
-
-  downstream.upstreamReactor = upstream;
-  downstream.currentTime = 0;
-  downstream.timeStep = 1;
-  downstream.speedUpFactor = 1;
-
-  let ticks = 0;
-  downstream.tick = () => {
-    ticks += 1;
-    return downstream.state;
-  };
-
-  downstream.updateState(DAY_MS);
-
-  assert.equal(ticks, 1);
-  assert.equal(downstream.Fs[0], 3);
-  assert.deepEqual(downstream.Cs_in[0], Array(13).fill(11));
-});

test/specificClass.test.js

@@ -0,0 +1,346 @@
+/**
+ * Tests for reactor specificClass (domain logic).
+ *
+ * Two reactor classes are exported: Reactor_CSTR and Reactor_PFR.
+ * Both extend a base Reactor class.
+ *
+ * Key methods tested:
+ *  - _calcOTR: oxygen transfer rate calculation
+ *  - _arrayClip2Zero: clip negative values to zero
+ *  - setInfluent / getEffluent: influent/effluent data flow
+ *  - setOTR: external OTR override
+ *  - tick (CSTR): forward Euler state update
+ *  - tick (PFR): finite difference state update
+ *  - registerChild: dispatches to measurement / reactor handlers
+ */
+
+const { Reactor_CSTR, Reactor_PFR } = require('../src/specificClass');
+
+// --------------- helpers ---------------
+
+const NUM_SPECIES = 13;
+
+function makeCSTRConfig(overrides = {}) {
+  return {
+    general: {
+      name: 'TestCSTR',
+      id: 'cstr-test-1',
+      logging: { enabled: false, logLevel: 'error' },
+    },
+    functionality: {
+      softwareType: 'reactor',
+      positionVsParent: 'atEquipment',
+    },
+    volume: 1000,
+    n_inlets: 1,
+    kla: 240,
+    timeStep: 1,      // 1 second
+    initialState: new Array(NUM_SPECIES).fill(1.0),
+    ...overrides,
+  };
+}
+
+function makePFRConfig(overrides = {}) {
+  return {
+    general: {
+      name: 'TestPFR',
+      id: 'pfr-test-1',
+      logging: { enabled: false, logLevel: 'error' },
+    },
+    functionality: {
+      softwareType: 'reactor',
+      positionVsParent: 'atEquipment',
+    },
+    volume: 200,
+    length: 10,
+    resolution_L: 10,
+    n_inlets: 1,
+    kla: 240,
+    alpha: 0.5,
+    timeStep: 1,
+    initialState: new Array(NUM_SPECIES).fill(0.1),
+    ...overrides,
+  };
+}
+
+// --------------- CSTR tests ---------------
+
+describe('Reactor_CSTR', () => {
+
+  describe('constructor / initialization', () => {
+    it('should create an instance and set state from initialState', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      expect(r).toBeDefined();
+      expect(r.state).toEqual(new Array(NUM_SPECIES).fill(1.0));
+    });
+
+    it('should initialize Fs and Cs_in arrays based on n_inlets', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig({ n_inlets: 3 }));
+      expect(r.Fs).toHaveLength(3);
+      expect(r.Cs_in).toHaveLength(3);
+      expect(r.Fs.every(v => v === 0)).toBe(true);
+    });
+
+    it('should store volume from config', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig({ volume: 500 }));
+      expect(r.volume).toBe(500);
+    });
+
+    it('should initialize temperature to 20', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      expect(r.temperature).toBe(20);
+    });
+  });
+
+  describe('_calcOTR()', () => {
+    let r;
+    beforeAll(() => { r = new Reactor_CSTR(makeCSTRConfig({ kla: 240 })); });
+
+    it('should return a positive value when S_O < saturation', () => {
+      const otr = r._calcOTR(0, 20);
+      expect(otr).toBeGreaterThan(0);
+    });
+
+    it('should return approximately zero when S_O equals saturation', () => {
+      // S_O_sat at T=20: 14.652 - 4.1022e-1*20 + 7.9910e-3*400 + 7.7774e-5*8000
+      const T = 20;
+      const S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T * T + 7.7774e-5 * T * T * T;
+      const otr = r._calcOTR(S_O_sat, T);
+      expect(otr).toBeCloseTo(0, 5);
+    });
+
+    it('should return a negative value when S_O > saturation (supersaturated)', () => {
+      const otr = r._calcOTR(100, 20);
+      expect(otr).toBeLessThan(0);
+    });
+
+    it('should use T=20 as default temperature', () => {
+      const otr1 = r._calcOTR(0);
+      const otr2 = r._calcOTR(0, 20);
+      expect(otr1).toBe(otr2);
+    });
+  });
+
+  describe('_arrayClip2Zero()', () => {
+    let r;
+    beforeAll(() => { r = new Reactor_CSTR(makeCSTRConfig()); });
+
+    it('should clip negative values to zero', () => {
+      expect(r._arrayClip2Zero([-5, 3, -1, 0, 7])).toEqual([0, 3, 0, 0, 7]);
+    });
+
+    it('should leave all-positive arrays unchanged', () => {
+      expect(r._arrayClip2Zero([1, 2, 3])).toEqual([1, 2, 3]);
+    });
+
+    it('should handle nested arrays (2D)', () => {
+      const result = r._arrayClip2Zero([[-1, 2], [3, -4]]);
+      expect(result).toEqual([[0, 2], [3, 0]]);
+    });
+
+    it('should handle a single scalar', () => {
+      expect(r._arrayClip2Zero(-5)).toBe(0);
+      expect(r._arrayClip2Zero(5)).toBe(5);
+    });
+  });
+
+  describe('setInfluent / getEffluent', () => {
+    it('should store influent data via setter', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig({ n_inlets: 2 }));
+      const input = {
+        payload: {
+          inlet: 0,
+          F: 100,
+          C: new Array(NUM_SPECIES).fill(5),
+        },
+      };
+      r.setInfluent = input;
+      expect(r.Fs[0]).toBe(100);
+      expect(r.Cs_in[0]).toEqual(new Array(NUM_SPECIES).fill(5));
+    });
+
+    it('should return effluent with the sum of Fs and the current state', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      r.Fs[0] = 50;
+      const eff = r.getEffluent;
+      expect(eff.topic).toBe('Fluent');
+      expect(eff.payload.F).toBe(50);
+      expect(eff.payload.C).toEqual(r.state);
+    });
+  });
+
+  describe('setOTR', () => {
+    it('should set the OTR value', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig({ kla: NaN }));
+      r.setOTR = { payload: 42 };
+      expect(r.OTR).toBe(42);
+    });
+  });
+
+  describe('tick()', () => {
+    it('should return a new state array of correct length', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      const result = r.tick(0.001);
+      expect(result).toHaveLength(NUM_SPECIES);
+    });
+
+    it('should not produce NaN values', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      r.Fs[0] = 10;
+      r.Cs_in[0] = new Array(NUM_SPECIES).fill(5);
+      const result = r.tick(0.001);
+      result.forEach(v => expect(Number.isNaN(v)).toBe(false));
+    });
+
+    it('should not produce negative concentrations', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      // Run multiple ticks
+      for (let i = 0; i < 100; i++) {
+        r.tick(0.001);
+      }
+      r.state.forEach(v => expect(v).toBeGreaterThanOrEqual(0));
+    });
+
+    it('should reach steady state with zero flow (concentrations change only via reaction)', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      // No inflow
+      const initial = [...r.state];
+      r.tick(0.0001);
+      // State should have changed due to reaction/OTR
+      const changed = r.state.some((v, i) => v !== initial[i]);
+      expect(changed).toBe(true);
+    });
+  });
+
+  describe('registerChild()', () => {
+    it('should not throw for "measurement" software type', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      // Passing null child will trigger warn but not crash
+      expect(() => r.registerChild(null, 'measurement')).not.toThrow();
+    });
+
+    it('should not throw for "reactor" software type', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      expect(() => r.registerChild(null, 'reactor')).not.toThrow();
+    });
+
+    it('should not throw for unknown software type', () => {
+      const r = new Reactor_CSTR(makeCSTRConfig());
+      expect(() => r.registerChild(null, 'unknown')).not.toThrow();
+    });
+  });
+});
+
+// --------------- PFR tests ---------------
+
+describe('Reactor_PFR', () => {
+
+  describe('constructor / initialization', () => {
+    it('should create an instance with 2D state grid', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      expect(r).toBeDefined();
+      expect(r.state).toHaveLength(10); // resolution_L = 10
+      expect(r.state[0]).toHaveLength(NUM_SPECIES);
+    });
+
+    it('should compute d_x = length / n_x', () => {
+      const r = new Reactor_PFR(makePFRConfig({ length: 10, resolution_L: 5 }));
+      expect(r.d_x).toBe(2);
+    });
+
+    it('should compute cross-sectional area A = volume / length', () => {
+      const r = new Reactor_PFR(makePFRConfig({ volume: 200, length: 10 }));
+      expect(r.A).toBe(20);
+    });
+
+    it('should initialize D (dispersion) to 0', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      expect(r.D).toBe(0);
+    });
+
+    it('should create derivative operators of correct size', () => {
+      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 8 }));
+      expect(r.D_op).toHaveLength(8);
+      expect(r.D_op[0]).toHaveLength(8);
+      expect(r.D2_op).toHaveLength(8);
+      expect(r.D2_op[0]).toHaveLength(8);
+    });
+  });
+
+  describe('setDispersion', () => {
+    it('should set the axial dispersion value', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      r.setDispersion = { payload: 0.5 };
+      expect(r.D).toBe(0.5);
+    });
+  });
+
+  describe('tick()', () => {
+    it('should return a 2D state grid of correct dimensions', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      r.D = 0.01;
+      const result = r.tick(0.0001);
+      expect(result).toHaveLength(10);
+      expect(result[0]).toHaveLength(NUM_SPECIES);
+    });
+
+    it('should not produce NaN values with small time step and dispersion', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      r.D = 0.01;
+      r.Fs[0] = 10;
+      r.Cs_in[0] = new Array(NUM_SPECIES).fill(5);
+      const result = r.tick(0.0001);
+      result.forEach(row => {
+        row.forEach(v => expect(Number.isNaN(v)).toBe(false));
+      });
+    });
+
+    it('should not produce negative concentrations', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      r.D = 0.01;
+      for (let i = 0; i < 10; i++) {
+        r.tick(0.0001);
+      }
+      r.state.forEach(row => {
+        row.forEach(v => expect(v).toBeGreaterThanOrEqual(0));
+      });
+    });
+  });
+
+  describe('_applyBoundaryConditions()', () => {
+    it('should apply Neumann BC at outlet (last = second to last)', () => {
+      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 5 }));
+      const state = Array.from({ length: 5 }, () => new Array(NUM_SPECIES).fill(1));
+      state[3] = new Array(NUM_SPECIES).fill(7);
+      r._applyBoundaryConditions(state);
+      // outlet BC: state[4] = state[3]
+      expect(state[4]).toEqual(new Array(NUM_SPECIES).fill(7));
+    });
+
+    it('should apply Neumann BC at inlet when no flow', () => {
+      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 5 }));
+      r.Fs[0] = 0;
+      const state = Array.from({ length: 5 }, () => new Array(NUM_SPECIES).fill(1));
+      state[1] = new Array(NUM_SPECIES).fill(3);
+      r._applyBoundaryConditions(state);
+      // No flow: state[0] = state[1]
+      expect(state[0]).toEqual(new Array(NUM_SPECIES).fill(3));
+    });
+  });
+
+  describe('_arrayClip2Zero() (inherited)', () => {
+    it('should clip 2D arrays correctly', () => {
+      const r = new Reactor_PFR(makePFRConfig());
+      const result = r._arrayClip2Zero([[-1, 2], [3, -4]]);
+      expect(result).toEqual([[0, 2], [3, 0]]);
+    });
+  });
+
+  describe('_calcOTR() (inherited)', () => {
+    it('should work the same as in CSTR', () => {
+      const r = new Reactor_PFR(makePFRConfig({ kla: 240 }));
+      const otr = r._calcOTR(0, 20);
+      expect(otr).toBeGreaterThan(0);
+    });
+  });
+});