Fix measurement event listener registration in Reactor class

package-lock.json

@@ -9,14 +9,14 @@
       "version": "0.0.1",
       "license": "SEE LICENSE",
       "dependencies": {
-        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git",
+        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git#fix-missing-references",
         "mathjs": "^14.5.2"
       }
     },
     "node_modules/@babel/runtime": {
-      "version": "7.28.2",
+      "version": "7.28.3",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.2.tgz",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.3.tgz",
-      "integrity": "sha512-KHp2IflsnGywDjBWDkR9iEqiWSpc8GIi0lgTT3mOElT0PP1tG26P4tmFI2YvAdzgq9RGyoHZQEIEdZy6Ec5xCA==",
+      "integrity": "sha512-9uIQ10o0WGdpP6GDhXcdOJPJuDgFtIDtN/9+ArJQ2NAfAmiuhTQdzkaTGR33v43GYS2UrSA0eX2pPPHoFVvpxA==",
       "license": "MIT",
       "engines": {
         "node": ">=6.9.0"
@@ -48,12 +48,12 @@
       "license": "MIT"
     },
     "node_modules/fraction.js": {
-      "version": "5.2.2",
+      "version": "5.3.4",
-      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.2.2.tgz",
+      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
-      "integrity": "sha512-uXBDv5knpYmv/2gLzWQ5mBHGBRk9wcKTeWu6GLTUEQfjCxO09uM/mHDrojlL+Q1mVGIIFo149Gba7od1XPgSzQ==",
+      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
       "license": "MIT",
       "engines": {
-        "node": ">= 12"
+        "node": "*"
       },
       "funding": {
         "type": "github",
@@ -62,7 +62,7 @@
     },
     "node_modules/generalFunctions": {
       "version": "1.0.0",
-      "resolved": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git#f13ee68938ea9d4b3a17ad90618c72634769c777",
+      "resolved": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git#302e12238745766a679ef11ca6ed5f4ea1548f87",
       "license": "SEE LICENSE"
     },
     "node_modules/javascript-natural-sort": {
@@ -72,9 +72,9 @@
       "license": "MIT"
     },
     "node_modules/mathjs": {
-      "version": "14.6.0",
+      "version": "14.7.0",
-      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.6.0.tgz",
+      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.7.0.tgz",
-      "integrity": "sha512-5vI2BLB5GKQmiSK9BH6hVkZ+GgqpdnOgEfmHl7mqVmdQObLynr63KueyYYLCQMzj66q69mV2XZZGQqqxeftQbA==",
+      "integrity": "sha512-RaMhb+9MSESjDZNox/FzzuFpIUI+oxGLyOy1t3BMoW53pGWnTzZtlucJ5cvbit0dIMYlCq00gNbW1giZX4/1Rg==",
       "license": "Apache-2.0",
       "dependencies": {
         "@babel/runtime": "^7.26.10",

package.json

@@ -27,7 +27,7 @@
     }
   },
   "dependencies": {
-    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git",
+    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git#fix-missing-references",
     "mathjs": "^14.5.2"
   }
 }

src/nodeClass.js

@@ -49,7 +49,7 @@ class nodeClass {
                     this.source.setDispersion = msg;
                     break;
                 case 'registerChild':
-                    // Register this node as a child of the parent node
+                    // Register this node as a parent of the child node
                     const childId = msg.payload;
                     const childObj = this.RED.nodes.getNode(childId); 
                     this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);

src/reaction_modules/asm3_class Koch.js

@@ -0,0 +1,211 @@
+const math = require('mathjs')
+
+/**
+ * ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters.
+ */
+class ASM3 {
+
+  constructor() {
+    /**
+     * Kinetic parameters for ASM3 at 20 C. Using Koch et al. 2000 parameters.
+     * @property {Object} kin_params - Kinetic parameters
+     */
+    this.kin_params = {
+      // Hydrolysis
+      k_H:      9.,   // hydrolysis rate constant       [g X_S g-1 X_H d-1]
+      K_X:      1.,   // hydrolysis saturation constant [g X_S g-1 X_H] 
+      // Heterotrophs
+      k_STO:    12.,  // storage rate constant          [g S_S g-1 X_H d-1]
+      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_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]
+      K_HCO:    0.1,  // saturation constant S_HCO      [mole HCO3 m-3]
+      b_H_O:    0.3,  // aerobic respiration rate       [d-1]
+      b_H_NO:   0.15, // anoxic respiration rate        [d-1]
+      b_STO_O:  0.3,  // aerobic respitation rate X_STO [d-1]
+      b_STO_NO: 0.15, // anoxic respitation rate X_STO  [d-1]
+      // Autotrophs
+      mu_A_max: 1.3,  // maximum specific growth rate   [d-1]
+      K_A_NH:   1.4,  // saturation constant S_NH3      [g NH3-N m-3] 
+      K_A_O:    0.5,  // saturation constant S_0        [g O2 m-3]
+      K_A_HCO:  0.5,  // saturation constant S_HCO      [mole HCO3 m-3]
+      b_A_O:    0.20, // aerobic respiration rate       [d-1]
+      b_A_NO:   0.10  // anoxic respiration rate        [d-1]
+    };
+
+    /**
+     * Stoichiometric and composition parameters for ASM3. Using Koch et al. 2000 parameters.
+     * @property {Object} stoi_params - Stoichiometric parameters
+     */
+    this.stoi_params = {
+      // Fractions
+      f_SI:     0.,   // fraction S_I from hydrolysis   [g S_I g-1 X_S]
+      f_XI:     0.2,  // fraction X_I from decomp X_H   [g X_I g-1 X_H]
+      // Yields
+      Y_STO_O:  0.80, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
+      Y_STO_NO: 0.70, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
+      Y_H_O:    0.80, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
+      Y_H_NO:   0.65, // anoxic yield X_H per X_STO     [g X_H g-1 X_STO]
+      Y_A:      0.24, // anoxic yield X_A per S_NO      [g X_A g-1 NO3-N]
+      // Composition (COD via DoR)
+      i_CODN:  -1.71, // COD content (DoR)              [g COD g-1 N2-N]
+      i_CODNO: -4.57, // COD content (DoR)              [g COD g-1 NO3-N]
+      // Composition (nitrogen)
+      i_NSI:    0.01, // nitrogen content S_I           [g N g-1 S_I]
+      i_NSS:    0.03, // nitrogen content S_S           [g N g-1 S_S]
+      i_NXI:    0.04, // nitrogen content X_I           [g N g-1 X_I]
+      i_NXS:    0.03, // nitrogen content X_S           [g N g-1 X_S]
+      i_NBM:    0.07, // nitrogen content X_H / X_A     [g N g-1 X_H / X_A]
+      // Composition (TSS)
+      i_TSXI:   0.75, // TSS content X_I                [g TS g-1 X_I]
+      i_TSXS:   0.75, // TSS content X_S                [g TS g-1 X_S]
+      i_TSBM:   0.90, // TSS content X_H / X_A          [g TS g-1 X_H / X_A]
+      i_TSSTO:  0.60, // TSS content X_STO (PHB based)  [g TS g-1 X_STO]
+      // Composition (charge)
+      i_cNH:    1/14, // charge per S_NH                [mole H+ g-1 NH3-N]
+      i_cNO:   -1/14  // charge per S_NO                [mole H+ g-1 NO3-N]
+    };
+
+    /**
+     * Temperature theta parameters for ASM3. Using Koch et al. 2000 parameters.
+     * These parameters are used to adjust reaction rates based on temperature.
+     * @property {Object} temp_params - Temperature theta parameters
+     */
+    this.temp_params = {
+      // Hydrolysis
+      theta_H:        0.04,
+      // Heterotrophs
+      theta_STO:      0.07,
+      theta_mu_H:     0.07,
+      theta_b_H_O:    0.07,
+      theta_b_H_NO:   0.07,
+      theta_b_STO_O:  this._compute_theta(0.1, 0.3, 10, 20),
+      theta_b_STO_NO: this._compute_theta(0.05, 0.15, 10, 20),
+      // Autotrophs
+      theta_mu_A:     0.105,
+      theta_b_A_O:    0.105,
+      theta_b_A_NO:   0.105
+    };
+
+    this.stoi_matrix = this._initialise_stoi_matrix();
+  }
+
+  /**
+   * Initialises the stoichiometric matrix for ASM3.
+   * @returns {Array} - The stoichiometric matrix for ASM3. (2D array)
+   */
+  _initialise_stoi_matrix() { // initialise stoichiometric matrix
+    const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params;
+
+    const stoi_matrix = Array(12);
+    // 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
+    stoi_matrix[0]  = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS];
+    stoi_matrix[1]  = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO];
+    stoi_matrix[2]  = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO];
+    stoi_matrix[3]  = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O];
+    stoi_matrix[4]  = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO];
+    stoi_matrix[5]  = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
+    stoi_matrix[6]  = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM];
+    stoi_matrix[7]  = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO];
+    stoi_matrix[8]  = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO];
+    stoi_matrix[9]  = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM];
+    stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
+    stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM];
+
+    return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix
+  }
+
+  /**
+   * Computes the Monod equation rate value for a given concentration and half-saturation constant.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species.
+   * @returns {number} - Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _monod(c, K) {
+    return c / (K + c);
+  }
+
+  /**
+   * Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species. 
+   * @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _inv_monod(c, K) {
+    return K / (K + c);
+  }
+
+  /**
+   * Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter.
+   * @param {number} k - Rate constant at 20 degrees Celcius.
+   * @param {number} theta - Theta parameter.
+   * @param {number} T - Temperature in Celcius.
+   * @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation.
+   */
+  _arrhenius(k, theta, T) {
+    return k * Math.exp(theta*(T-20));
+  }
+
+  /**
+   * Computes the temperature theta parameter based on two rate constants and their corresponding temperatures.
+   * @param {number} k1 - Rate constant at temperature T1.
+   * @param {number} k2 - Rate constant at temperature T2.
+   * @param {number} T1 - Temperature T1 in Celcius.
+   * @param {number} T2 - Temperature T2 in Celcius.
+   * @returns {number} - Theta parameter.
+   */
+  _compute_theta(k1, k2, T1, T2) {
+    return Math.log(k1/k2)/(T1-T2);
+  }
+
+  /**
+   * Computes the reaction rates for each process reaction based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Reaction rates for each process reaction.
+   */
+  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 { 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;
+
+    // Hydrolysis
+    rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H;
+
+    // Heterotrophs
+    rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H;
+    rates[2] = this._arrhenius(k_STO, theta_STO, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H;
+    rates[3] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
+    rates[4] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H;
+    rates[5] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H;
+    rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO;
+    
+    // Autotrophs
+    rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A;
+    rates[10] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A;
+    rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A;
+    
+    return rates;
+  }
+
+  /**
+   * Computes the change in concentrations of reaction species based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Change in reaction species concentrations.
+   */
+  compute_dC(state, T = 20) { // compute changes in concentrations
+    // 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
+    return math.multiply(this.stoi_matrix, this.compute_rates(state, T));
+  }
+}
+
+module.exports = ASM3;

src/specificClass.js

@@ -44,18 +44,6 @@ class Reactor {
     this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
   }
 
-  updateMeasurement(variant, subType, value, position) {
-    this.logger.debug(`---------------------- updating ${subType} ------------------ `);
-    switch (subType) {
-      case "temperature":
-        this.temperature = value;
-        break;
-      default:
-        this.logger.error(`Type '${subType}' not recognized for measured update.`);
-        return;
-    }
-  }
-
   /**
    * Setter for influent data.
    * @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
@@ -109,6 +97,76 @@ class Reactor {
     }
   }
 
+  registerChild(child, softwareType) {
+    switch (softwareType) {
+      case "measurement":
+        this.logger.debug(`Registering measurement child.`);
+        this._connectMeasurement(child);
+        break;
+      case "reactor":
+        this.logger.debug(`Registering reactor child.`);
+        this._connectReactor(child);
+        break;
+
+      default:
+        this.logger.error(`Unrecognized softwareType: ${softwareType}`);
+    }
+  }
+
+  _connectMeasurement(measurement) {
+    if (!measurement) {
+      this.logger.warn("Invalid measurement provided.");
+      return;
+    }
+
+    const position = measurement.config.functionality.positionVsParent;
+    const measurementType = measurement.config.asset.type;
+    const key = `${measurementType}_${position}`;
+    const eventName = `${measurementType}.measured.${position}`;
+
+    // Register event listener for measurement updates
+    this.measurements.emitter.on(eventName, (eventData) => {
+      this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
+
+      // Store directly in parent's measurement container
+      this.measurements
+        .type(measurementType)
+        .variant("measured")
+        .position(position)
+        .value(eventData.value, eventData.timestamp, eventData.unit);
+      
+      this._updateMeasurement(measurementType, eventData.value, position, eventData);
+    });
+  }
+
+
+  _connectReactor(reactor) {
+    if (!reactor) {
+      this.logger.warn("Invalid reactor provided.");
+      return;
+    }
+
+    this.upstreamReactor = reactor;
+
+    reactor.emitter.on("stateChange", (data) => {
+      this.logger.debug(`State change of upstream reactor detected.`);
+      this.updateState(data);
+    });
+  }
+
+  
+  _updateMeasurement(measurementType, value, position, context) {
+    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
+    switch (measurementType) {
+      case "temperature":
+        this.temperature = value;
+        break;
+      default:
+        this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
+        return;
+    }
+  }
+
   /**
    * Update the reactor state based on the new time.
    * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
@@ -255,14 +313,14 @@ class Reactor_PFR extends Reactor {
     return stateNew;
   }
 
-  updateMeasurement(variant, subType, value, position) {
+  _updateMeasurement(measurementType, value, position, context) {
-    switch(subType) {
+    switch(measurementType) {
       case "oxygen":
         grid_pos = Math.round(position * this.n_x);
         this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
-        return;
+        break;
     }
-    super.updateMeasurement(variant, subType, value, position);
+    super._updateMeasurement(measurementType, value, position, context);
   }
 
   /**