Merge remote-tracking branch 'origin/main' into dev-Rene

# Conflicts:
#	additional_nodes/recirculation-pump.js
#	additional_nodes/settling-basin.js
#	reactor.html
#	src/nodeClass.js
#	src/reaction_modules/asm3_class Koch.js
#	src/reaction_modules/asm3_class.js
#	src/specificClass.js

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:

reactor.html

@@ -40,6 +40,8 @@
 
             timeStep: { value: 1, required: true },
             speedUpFactor: { value: 1 },
+            processOutputFormat: { value: "process" },
+            dbaseOutputFormat: { value: "influxdb" },
 
             enableLog: { value: false },
             logLevel: { value: "error" },
@@ -252,6 +254,23 @@
         <label for="node-input-speedUpFactor"><i class="fa fa-tag"></i> Speed-up factor</label>
         <input type="text" id="node-input-speedUpFactor" placeholder="1 = real-time">
     </div>
+    <h3>Output Formats</h3>
+    <div class="form-row">
+        <label for="node-input-processOutputFormat"><i class="fa fa-random"></i> Process Output</label>
+        <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 -->
 	<div id="logger-fields-placeholder"></div>

src/nodeClass.js

@@ -1,5 +1,5 @@
 const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
-const { outputUtils } = require('generalFunctions');
+const { outputUtils, configManager } = require('generalFunctions');
 
 const REACTOR_SPECIES = [
     'S_O',
@@ -90,24 +90,14 @@ class nodeClass {
     }
 
     /**
-     * Parse node configuration
+     * Parse node configuration using ConfigManager
      * @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),
@@ -132,7 +122,7 @@ class nodeClass {
             ],
             timeStep: parseFloat(uiConfig.timeStep),
             speedUpFactor: Number(uiConfig.speedUpFactor) || 1
-        }
+        });
     }
 
     /**

src/reaction_modules/asm3_class Koch.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/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 = {
@@ -169,7 +169,6 @@ 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
@@ -203,11 +202,11 @@ 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;
@@ -325,7 +324,7 @@ class Reactor_PFR extends Reactor {
     let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
     let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
 
-    (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
+    (Pe_local >= 2) && this.logger.warn(`Local Peclet number (${Pe_local}) is too high! Increase reactor resolution.`);
     (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
 
     if(DEBUG) {

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);
+    });
+  });
+});