Add warnings for reactor child positioning and grid sizing discrepancies

LICENSE

@@ -1,9 +1,190 @@
-MIT License
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+                                                         Appendix
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+— European Union Public Licence (EUPL) v. 1.1, v. 1.2
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README.md

@@ -1,3 +1,17 @@
-# asm3
+# reactor
+
+Reactor: Advanced Hydraulic Tank & Biological Process Simulator
+
+A comprehensive reactor class for wastewater treatment simulation featuring plug flow hydraulics, ASM1-ASM3 biological modeling, and multi-sectional concentration tracking. Implements hydraulic retention time calculations, dispersion modeling, and real-time biological reaction kinetics for accurate process simulation.
+
+Key Features:
+
+Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
+ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
+Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
+Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves
+Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
+Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
+Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
+Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.
 
-Implementation of the asm3 model (doi:10.1016/S0273-1223(98)00785-9)

package-lock.json

@@ -1,22 +1,22 @@
 {
-  "name": "asm3",
+  "name": "reactor",
   "version": "0.0.1",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
-      "name": "asm3",
+      "name": "reactor",
       "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/RnD/generalFunctions.git",
         "mathjs": "^14.5.2"
       }
     },
     "node_modules/@babel/runtime": {
-      "version": "7.28.2",
+      "version": "7.28.4",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.2.tgz",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
-      "integrity": "sha512-KHp2IflsnGywDjBWDkR9iEqiWSpc8GIi0lgTT3mOElT0PP1tG26P4tmFI2YvAdzgq9RGyoHZQEIEdZy6Ec5xCA==",
+      "integrity": "sha512-Q/N6JNWvIvPnLDvjlE1OUBLPQHH6l3CltCEsHIujp45zQUSSh8K+gHnaEX45yAT1nyngnINhvWtzN+Nb9D8RAQ==",
       "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/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
       "license": "SEE LICENSE"
     },
     "node_modules/javascript-natural-sort": {
@@ -72,9 +72,9 @@
       "license": "MIT"
     },
     "node_modules/mathjs": {
-      "version": "14.6.0",
+      "version": "14.8.0",
-      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.6.0.tgz",
+      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
-      "integrity": "sha512-5vI2BLB5GKQmiSK9BH6hVkZ+GgqpdnOgEfmHl7mqVmdQObLynr63KueyYYLCQMzj66q69mV2XZZGQqqxeftQbA==",
+      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
       "license": "Apache-2.0",
       "dependencies": {
         "@babel/runtime": "^7.26.10",

package.json

@@ -1,10 +1,10 @@
 {
-  "name": "asm3",
+  "name": "reactor",
   "version": "0.0.1",
   "description": "Implementation of the asm3 model for Node-Red",
   "repository": {
     "type": "git",
-    "url": "https://gitea.centraal.wbd-rd.nl/p.vanderwilt/asm3.git"
+    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
   },
   "keywords": [
     "asm3",
@@ -15,19 +15,19 @@
   ],
   "license": "SEE LICENSE",
   "author": "P.R. van der Wilt",
-  "main": "advancedReactor.js",
+  "main": "reactor.js",
   "scripts": {
-    "test": "node advancedReactor.js"
+    "test": "node reactor.js"
   },
   "node-red": {
     "nodes": {
-      "advancedReactor": "advancedReactor.js",
+      "reactor": "reactor.js",
       "recirculation-pump": "additional_nodes/recirculation-pump.js",
       "settling-basin": "additional_nodes/settling-basin.js"
     }
   },
   "dependencies": {
-    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git",
+    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
     "mathjs": "^14.5.2"
   }
 }

reactor.html

@@ -1,7 +1,7 @@
-<script src="/advancedReactor/menu.js"></script>
+<script src="/reactor/menu.js"></script>
 
 <script type="text/javascript">
-    RED.nodes.registerType("advancedReactor", {
+    RED.nodes.registerType("reactor", {
         category: "WWTP",
         color: "#c4cce0",
         defaults: {
@@ -28,6 +28,8 @@
             X_A_init: { value: 0.001, required: true },
             X_TS_init: { value: 125.0009, required: true },
 
+            timeStep: { value: 1, required: true },
+
             enableLog: { value: false },
             logLevel: { value: "error" },
 
@@ -39,13 +41,13 @@
         outputLabels: ["process", "dbase", "parent"],
         icon: "font-awesome/fa-recycle",
         label: function() {
-            return this.name || "advancedReactor";
+            return this.name || "Reactor";
         },
         oneditprepare: function() {
             // wait for the menu scripts to load
             const waitForMenuData = () => {
-                if (window.EVOLV?.nodes?.advancedReactor?.initEditor) {
+                if (window.EVOLV?.nodes?.reactor?.initEditor) {
-                    window.EVOLV.nodes.advancedReactor.initEditor(this);
+                    window.EVOLV.nodes.reactor.initEditor(this);
                 } else {
                     setTimeout(waitForMenuData, 50);
                 }
@@ -99,6 +101,10 @@
                 type:"num",
                 types:["num"]
             })
+            $("#node-input-timeStep").typedInput({
+                type:"num",
+                types:["num"]
+            })
             // Set initial visibility on dialog open
             const initialType = $("#node-input-reactor_type").typedInput("value");
             if (initialType === "CSTR") {
@@ -109,8 +115,8 @@
         },
         oneditsave: function() {
             // save logger fields
-            if (window.EVOLV?.nodes?.['advancedReactor']?.loggerMenu?.saveEditor) {
+            if (window.EVOLV?.nodes?.reactor?.loggerMenu?.saveEditor) {
-                window.EVOLV.nodes['advancedReactor'].loggerMenu.saveEditor(this);
+                window.EVOLV.nodes.reactor.loggerMenu.saveEditor(this);
             }
 
             // save position field
@@ -130,7 +136,7 @@
     });
 </script>
 
-<script type="text/html" data-template-name="advancedReactor">
+<script type="text/html" data-template-name="reactor">
     <div class="form-row">
         <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
         <input type="text" id="node-input-name" placeholder="Name">
@@ -222,6 +228,11 @@
         <label for="node-input-X_TS_init"><i class="fa fa-tag"></i> Initial total suspended solids [g TSS m-3]</label>
         <input type="text" id="node-input-X_TS_init" class="concentrations">
     </div>
+    <h2> Simulation parameters </h2>
+    <div class="form-row">
+        <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>
 
     <!-- Logger fields injected here -->
 	<div id="logger-fields-placeholder"></div>
@@ -232,6 +243,6 @@
 
 </script>
 
-<script type="text/html" data-help-name="advancedReactor">
+<script type="text/html" data-help-name="reactor">
     <p>New reactor node</p>
 </script>

reactor.js

@@ -1,4 +1,4 @@
-const nameOfNode = "advancedReactor"; // name of the node, should match file name and node type in Node-RED
+const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
 const nodeClass = require('./src/nodeClass.js'); // node class
 const { MenuManager } = require('generalFunctions');
 

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);
@@ -104,7 +104,8 @@ class nodeClass {
                 parseFloat(uiConfig.X_STO_init),
                 parseFloat(uiConfig.X_A_init),
                 parseFloat(uiConfig.X_TS_init)
-            ]
+            ],
+            timeStep: parseFloat(uiConfig.timeStep)
         }
     }
 

src/specificClass.js

@@ -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();
 
@@ -40,20 +45,8 @@ class Reactor {
     this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
 
     this.currentTime = Date.now(); // milliseconds since epoch [ms]
-    this.timeStep = 1 / (24*60*15); // time step [d]
+    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
-  }
-
-  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;
-    }
   }
 
   /**
@@ -109,6 +102,86 @@ 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: ${softwareType}`);
+    }
+  }
+
+  _connectMeasurement(measurementChild) {
+    if (!measurementChild) {
+      this.logger.warn("Invalid measurement provided.");
+      return;
+    }
+
+    const position = measurementChild.config.functionality.positionVsParent;
+    const measurementType = measurementChild.config.asset.type;
+    const eventName = `${measurementType}.measured.${position}`;
+
+    // Register event listener for measurement updates
+    measurementChild.measurements.emitter.on(eventName, (eventData) => {
+      this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
+
+      // Store directly in parent's measurement container
+      this.measurements
+        .type(measurementType)
+        .variant("measured")
+        .position(position)
+        .value(eventData.value, eventData.timestamp, eventData.unit);
+      
+      this._updateMeasurement(measurementType, eventData.value, position, eventData);
+    });
+  }
+
+
+  _connectReactor(reactorChild) {
+    if (!reactorChild) {
+      this.logger.warn("Invalid reactor provided.");
+      return;
+    }
+
+    if (reactorChild.functionality.positionVsParent != "upstream") {
+      this.logger.warn("Reactor children of reactors should always be upstream.");
+    }
+
+    if (math.abs(reactorChild.d_x - this.d_x) / this.d_x < 0.025) {
+      this.logger.warn("Significant grid sizing discrepancies between adjacent reactors! Change resolutions to match reactors grid step, or implement boundary value interpolation.");
+    }
+
+    this.upstreamReactor = reactorChild;
+    reactorChild.downstreamReactor = this;
+
+    reactorChild.emitter.on("stateChange", (data) => {
+      this.logger.debug(`State change of upstream reactor detected.`);
+      this.updateState(data);
+    });
+  }
+
+  
+  _updateMeasurement(measurementType, value, position, context) {
+    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
+    switch (measurementType) {
+      case "temperature":
+        if (position == "atEquipment") {
+          this.temperature = value;
+        }
+        break;
+      default:
+        this.logger.error(`Type '${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.
@@ -181,11 +254,15 @@ 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();
@@ -197,15 +274,16 @@ class Reactor_PFR extends Reactor {
    * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
    */
   set setDispersion(input) {
-    this.D = input.payload;
+    this.D = this._constrainDispersion(input.payload);
   }
 
   updateState(newTime) {
     super.updateState(newTime);
-    let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
+    // let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
+    this.D = this._constrainDispersion(this.D);
     let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
 
-    (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
+    // (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${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) {
@@ -223,25 +301,26 @@ 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");
@@ -252,74 +331,70 @@ class Reactor_PFR extends Reactor {
     }
 
     this.state = this._arrayClip2Zero(stateNew);
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
     return stateNew;
   }
 
-  updateMeasurement(variant, subType, value, position) {
+  _updateMeasurement(measurementType, value, position, context) {
-    switch(subType) {
+    switch(measurementType) {
-      case "oxygen":
+      case "quantity (oxygen)":
-        grid_pos = Math.round(position * 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
-        return;
+        break;
+      default:
+        super._updateMeasurement(measurementType, value, position, context);
     }
-    super.updateMeasurement(variant, subType, value, position);
   }
 
   /**
    * 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 (this.upstreamReactor) {
+      for (let i = 0; i < BC_PADDING; i++) {
+        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
+      }
+    } else {
       if (math.sum(this.Fs) > 0) { // Danckwerts BC
         const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
         const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
-      state[0] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, state[1])));
+        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 {
-      state[0] = state[1];
+        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)
-    state[this.n_x-1] = state[this.n_x-2];
+      for (let i = 0; i < BC_PADDING; i++) {
+        this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
+      }
+    }
   }
 
   /**
    * 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 NearBoundary = Array(this.n_x).fill(0.0);
+    // set by BCs elsewhere
-        NearBoundary[0] = -1/4;
+    D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
-        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;
-    }
   }
 
   /**
@@ -327,14 +402,24 @@ 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;
   }
+
+  _constrainDispersion(D) {
+    const Dmin = math.sum(this.Fs) * this.d_x / (1.999 * this.A);
+    if (D < Dmin) {
+      this.logger.warn(`Local Péclet number too high! Constraining given dispersion (${D}) to minimal value (${Dmin}).`);
+      return Dmin;
+    }
+    return D;
+  }
 }
 
 module.exports = { Reactor_CSTR, Reactor_PFR };