Refactor measurement position assignment and update grid position calculation in Reactor classes to align with new generalFunctions

additional_nodes/recirculation-pump.js

@@ -3,12 +3,13 @@ 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);
@@ -23,7 +24,6 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
-                }
                 case "clock":
                     break;
                 default:

additional_nodes/settling-basin.js

@@ -3,12 +3,13 @@ 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;
@@ -40,7 +41,6 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
-                }
                 case "clock":
                     break;
                 default:

src/nodeClass.js

@@ -1,5 +1,4 @@
 const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
-const { configManager } = require('generalFunctions');
 
 
 class nodeClass {
@@ -49,15 +48,14 @@ class nodeClass {
                 case "Dispersion":
                     this.source.setDispersion = msg;
                     break;
-                case 'registerChild': {
+                case 'registerChild':
                     // Register this node as a parent of the child node
                     const childId = msg.payload;
-                    const childObj = this.RED.nodes.getNode(childId);
+                    const childObj = this.RED.nodes.getNode(childId); 
                     this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
                     break;
-                }
                 default:
-                    this.source.logger.warn(`Unknown topic: ${msg.topic}`);
+                    console.log("Unknown topic: " + msg.topic);
             }
 
             if (done) {
@@ -71,10 +69,20 @@ class nodeClass {
      * @param {object} uiConfig Config set in UI in node-red
      */
     _loadConfig(uiConfig) {
-        const cfgMgr = new configManager();
+        this.config = {
-
+            general: {
-        // Build config: base sections + reactor-specific domain config
+                name: uiConfig.name || this.name,
-        this.config = cfgMgr.buildConfig('reactor', uiConfig, this.node.id, {
+                id: 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),
@@ -98,7 +106,7 @@ class nodeClass {
                 parseFloat(uiConfig.X_TS_init)
             ],
             timeStep: parseFloat(uiConfig.timeStep)
-        });
+        }
     }
 
     /**
@@ -129,7 +137,7 @@ class nodeClass {
                 new_reactor = new Reactor_PFR(this.config);
                 break;
             default:
-                throw new Error(`Unknown reactor type: ${this.config.reactor_type}`);
+                console.warn("Unknown reactor type: " + uiConfig.reactor_type);
         }
 
         this.source = new_reactor; // protect from reassignment

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:      10.0, // saturation constant S_s        [g COD m-3]
+      K_S:      10.,  // 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_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
+    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 { 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_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
+    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 { 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, POSITIONS } = require('generalFunctions');
+const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
 const EventEmitter = require('events');
 
 const mathConfig = {
@@ -12,6 +12,7 @@ const math = create(all, mathConfig);
 
 const S_O_INDEX = 0;
 const NUM_SPECIES = 13;
+const BC_PADDING = 2;
 const DEBUG = false;
 
 class Reactor {
@@ -27,6 +28,10 @@ class Reactor {
     this.measurements = new MeasurementContainer();
     this.upstreamReactor = null;
     this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
+    this.parent = []; // Gets assigned via child registration
+
+    this.upstreamReactor = null;
+    this.downstreamReactor = null;
 
     this.asm = new ASM3();
 
@@ -41,7 +46,7 @@ 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 = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
+    this.speedUpFactor = 100; // speed up factor for simulation, 60 means 1 minute per simulated second
   }
 
   /**
@@ -113,23 +118,18 @@ class Reactor {
     }
   }
 
-  _connectMeasurement(measurement) {
+  _connectMeasurement(measurementChild) {
-    if (!measurement) {
+    if (!measurementChild) {
       this.logger.warn("Invalid measurement provided.");
       return;
     }
 
-    let position;
+    const position = measurementChild.config.functionality.positionVsParent;
-    if (measurement.config.functionality.distance !== 'undefined') {
+    const measurementType = measurementChild.config.asset.type;
-      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) => {
+    measurementChild.measurements.emitter.on(eventName, (eventData) => {
       this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
 
       // Store directly in parent's measurement container
@@ -144,26 +144,27 @@ class Reactor {
   }
 
 
-  _connectReactor(reactor) {
+  _connectReactor(reactorChild) {
-    if (!reactor) {
+    if (!reactorChild) {
       this.logger.warn("Invalid reactor provided.");
       return;
     }
 
-    this.upstreamReactor = reactor;
+    this.upstreamReactor = reactorChild;
+    reactorChild.downstreamReactor = this;
 
-    reactor.emitter.on("stateChange", (data) => {
+    reactorChild.emitter.on("stateChange", (data) => {
       this.logger.debug(`State change of upstream reactor detected.`);
       this.updateState(data);
     });
   }
 
   
-  _updateMeasurement(measurementType, value, position, _context) {
+  _updateMeasurement(measurementType, value, position, context) {
     this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
     switch (measurementType) {
       case "temperature":
-        if (position == POSITIONS.AT_EQUIPMENT) {
+        if (position == "atEquipment") {
           this.temperature = value;
         }
         break;
@@ -245,11 +246,15 @@ class Reactor_PFR extends Reactor {
 
     this.alpha = config.alpha;
 
-    this.state = Array.from(Array(this.n_x), () => config.initialState.slice())
+    this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
+    this.extendedState = Array.from(Array(this.n_x + 2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
+
+    // initialise extended state
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
 
     this.D = 0.0; // axial dispersion [m2 d-1]
 
-    this.D_op = this._makeDoperator(true, true);
+    this.D_op = this._makeDoperator();
     assertNoNaN(this.D_op, "Derivative operator");
 
     this.D2_op = this._makeD2operator();
@@ -287,25 +292,26 @@ class Reactor_PFR extends Reactor {
    * @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);
+    this._applyBoundaryConditions();
-    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 dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
-    const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
+    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.extendedState);
+    const reaction = this.extendedState.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
+    const transfer = Array.from(Array(this.n_x+2*BC_PADDING), () => 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++) {
+      for (let i = BC_PADDING+1; i < BC_PADDING+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++) {
+    for (let i = BC_PADDING+1; i < BC_PADDING+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);
+        transfer[i][S_O_INDEX] = this._calcOTR(this.extendedState[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 dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
 
     const stateNew = math.add(this.state, dC_total);
-    this._applyBoundaryConditions(stateNew);
 
     if (DEBUG) {
       assertNoNaN(dispersion, "dispersion");
@@ -316,18 +322,18 @@ class Reactor_PFR extends Reactor {
     }
 
     this.state = this._arrayClip2Zero(stateNew);
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
     return stateNew;
   }
 
-  _updateMeasurement(measurementType, value, position, _context) {
+  _updateMeasurement(measurementType, value, position, context) {
     switch(measurementType) {
-      case "quantity (oxygen)": {
+      case "quantity (oxygen)":
-        let grid_pos = Math.round(position / this.config.length * this.n_x);
+        let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
         this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
         break;
-      }
       default:
-        super._updateMeasurement(measurementType, value, position, _context);
+        super._updateMeasurement(measurementType, value, position, context);
     }
   }
 
@@ -335,57 +341,51 @@ class Reactor_PFR extends Reactor {
    * 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) {
+  _applyBoundaryConditions() {
-    if (math.sum(this.Fs) > 0) { // Danckwerts BC
+    if (this.upstreamReactor) {
-      const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
+      for (let i = 0; i < BC_PADDING; i++) {
-      const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
+        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
-      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];
+      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);
+        this.extendedState[BC_PADDING] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, this.extendedState[BC_PADDING+1])));
+        this.extendedState[BC_PADDING-1] = math.add(math.multiply(2, this.extendedState[BC_PADDING]), math.multiply(-2, this.extendedState[BC_PADDING+2]), this.extendedState[BC_PADDING+3]);
+      } else {
+        for (let i = 0; i < BC_PADDING; i++) {
+          this.extendedState[i] = this.extendedState[BC_PADDING];
+        }
+      }
+    }
+
+    if (this.downstreamReactor) {
+      for (let i = 0; i < BC_PADDING; i++) {
+        this.extendedState[this.n_x+BC_PADDING+i] = this.downstreamReactor.state[i];
+      }
+    } else {
+      // Neumann BC (no flux)
+      for (let i = 0; i < BC_PADDING; i++) {
+        this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
+      }
     }
-    // Neumann BC (no flux)
-    state[this.n_x-1] = state[this.n_x-2];
   }
 
   /**
    * 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
+  _makeDoperator() { // create gradient operator
-    if (higher_order) {
+    const D_size = this.n_x+2*BC_PADDING;
-      if (central) {
+    const I = math.resize(math.diag(Array(D_size).fill(1/12), -2), [D_size, D_size]);
-        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(D_size).fill(-2/3), -1), [D_size, D_size]);
-        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(D_size).fill(2/3), 1), [D_size, D_size]);
-        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(D_size).fill(-1/12), 2), [D_size, D_size]);
-        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 D = math.add(I, A, B, C);
+    // set by BCs elsewhere
-        const NearBoundary = Array(this.n_x).fill(0.0);
+    D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
-        NearBoundary[0] = -1/4;
+    return D;
-        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;
-    }
   }
 
   /**
@@ -393,12 +393,13 @@ class Reactor_PFR extends Reactor {
    * @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 D_size = this.n_x+2*BC_PADDING;
-    const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]);
+    const I = math.diag(Array(D_size).fill(-2), 0);
-    const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]);
+    const A = math.resize(math.diag(Array(D_size).fill(1), 1), [D_size, D_size]);
+    const B = math.resize(math.diag(Array(D_size).fill(1), -1), [D_size, D_size]);
     const D2 = math.add(I, A, B);
-    D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
+    // set by BCs elsewhere
-    D2[this.n_x - 1] = Array(this.n_x).fill(0);
+    D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
     return D2;
   }
 }

test/specificClass.test.js

@@ -1,346 +0,0 @@
-/**
- * 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);
-    });
-  });
-});