changed colours and icon based on s88

reactor.html

@@ -1,9 +1,19 @@
+<!--
+| S88-niveau             | Primair (blokkleur) | Tekstkleur |
+| ---------------------- | ------------------- | ---------- |
+| **Area**               | `#0f52a5`           | wit        |
+| **Process Cell**       | `#0c99d9`           | wit        |
+| **Unit**               | `#50a8d9`           | zwart      |
+| **Equipment (Module)** | `#86bbdd`           | zwart      |
+| **Control Module**     | `#a9daee`           | zwart      |
+
+-->
 <script src="/reactor/menu.js"></script>
 
 <script type="text/javascript">
     RED.nodes.registerType("reactor", {
-        category: "WWTP",
-        color: "#c4cce0",
+        category: "EVOLV",
+        color: "#50a8d9",
         defaults: {
             name: { value: "" },
             reactor_type: { value: "CSTR", required: true },
@@ -39,7 +49,7 @@
         outputs: 3,
         inputLabels: ["input"],
         outputLabels: ["process", "dbase", "parent"],
-        icon: "font-awesome/fa-recycle",
+        icon: "font-awesome/fa-flask",
         label: function() {
             return this.name || "Reactor";
         },

src/specificClass.js

@@ -12,7 +12,6 @@ const math = create(all, mathConfig);
 
 const S_O_INDEX = 0;
 const NUM_SPECIES = 13;
-const BC_PADDING = 2;
 const DEBUG = false;
 
 class Reactor {
@@ -28,11 +27,6 @@ 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.returnPump = null;
 
     this.asm = new ASM3();
 
@@ -47,7 +41,7 @@ class Reactor {
 
     this.currentTime = Date.now(); // milliseconds since epoch [ms]
     this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
-    this.speedUpFactor = 100; // speed up factor for simulation, 60 means 1 minute per simulated second
+    this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
   }
 
   /**
@@ -73,17 +67,10 @@ class Reactor {
    * @returns {object} Effluent data object (msg), defaults to inlet 0.
    */
   get getEffluent() { // getter for Effluent, defaults to inlet 0
-    const Cs = isArray(this.state.at(-1)) ? this.state.at(-1) : this.state;
-    const effluent = [{ topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: Cs }, timestamp: this.currentTime }];
-    if (this.returnPump) {
-      const recirculationFlow = this.returnPump.measurements.type("flow").variant("measured").position("atEquipment").getCurrentValue();
-      // constrain flow to prevent negatives
-      const F_main = Math.max(effluent[0].payload.F - recirculationFlow, 0);
-      const F_sidestream = effluent[0].payload.F < recirculationFlow ? effluent[0].payload.F : recirculationFlow;
-      effluent[0].payload.F = F_main;
-      effluent.push({ topic: "Fluent", payload: { inlet: 1, F: F_sidestream, C: Cs }, timestamp: this.currentTime });
+    if (isArray(this.state.at(-1))) {
+      return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
     }
-    return effluent;
+    return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
   }
 
   /**
@@ -113,35 +100,37 @@ class Reactor {
   registerChild(child, softwareType) {
     switch (softwareType) {
       case "measurement":
-        this.logger.debug(`Registering measurement child...`);
+        this.logger.debug(`Registering measurement child.`);
         this._connectMeasurement(child);
         break;
       case "reactor":
-        this.logger.debug(`Registering reactor child...`);
+        this.logger.debug(`Registering reactor child.`);
         this._connectReactor(child);
         break;
-      case "machine":
-        this.logger.debug(`Registering rotating machine child...`);
-        this._connectRotatingMachine(child);
-        break;
 
       default:
         this.logger.error(`Unrecognized softwareType: ${softwareType}`);
     }
   }
 
-  _connectMeasurement(measurementChild) {
-    if (!measurementChild) {
+  _connectMeasurement(measurement) {
+    if (!measurement) {
       this.logger.warn("Invalid measurement provided.");
       return;
     }
 
-    const position = measurementChild.config.functionality.positionVsParent;
-    const measurementType = measurementChild.config.asset.type;
+    let position;
+    if (measurement.config.functionality.distance !== 'undefined') {
+      position = measurement.config.functionality.distance;
+    } else {
+      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
-    measurementChild.measurements.emitter.on(eventName, (eventData) => {
+    measurement.measurements.emitter.on(eventName, (eventData) => {
       this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
 
       // Store directly in parent's measurement container
@@ -156,40 +145,20 @@ class Reactor {
   }
 
 
-  _connectReactor(reactorChild) {
-    if (!reactorChild) {
+  _connectReactor(reactor) {
+    if (!reactor) {
       this.logger.warn("Invalid reactor provided.");
       return;
     }
 
-    if (reactorChild.config.functionality.positionVsParent != "upstream") {
-      this.logger.warn("Reactor children of reactors should always be upstream.");
-    }
+    this.upstreamReactor = reactor;
 
-    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.");
-    }
-
-    // set upstream and downstream reactor variable in current and child nodes respectively for easy access
-    this.upstreamReactor = reactorChild;
-    reactorChild.downstreamReactor = this;
-
-    reactorChild.emitter.on("stateChange", (data) => {
+    reactor.emitter.on("stateChange", (data) => {
       this.logger.debug(`State change of upstream reactor detected.`);
       this.updateState(data);
     });
   }
 
-  _connectRotatingMachine(rotatingMachineChild) {
-    if (!rotatingMachineChild) {
-      this.logger.warn("Invalid rotating machine provided.");
-      return;
-    }
-
-    if (rotatingMachineChild.config.functionality.positionVsParent == "downstream") {
-      this.returnPump = rotatingMachineChild;
-    }
-  }
   
   _updateMeasurement(measurementType, value, position, context) {
     this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
@@ -213,7 +182,7 @@ class Reactor {
     const day2ms = 1000 * 60 * 60 * 24;
 
     if (this.upstreamReactor) {
-      this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
+      this.setInfluent = this.upstreamReactor.getEffluent;
     }
 
     let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms));
@@ -277,15 +246,11 @@ class Reactor_PFR extends Reactor {
 
     this.alpha = config.alpha;
 
-    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.state = Array.from(Array(this.n_x), () => config.initialState.slice())
 
     this.D = 0.0; // axial dispersion [m2 d-1]
 
-    this.D_op = this._makeDoperator();
+    this.D_op = this._makeDoperator(true, true);
     assertNoNaN(this.D_op, "Derivative operator");
 
     this.D2_op = this._makeD2operator();
@@ -297,16 +262,15 @@ class Reactor_PFR extends Reactor {
    * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
    */
   set setDispersion(input) {
-    this.D = this._constrainDispersion(input.payload);
+    this.D = input.payload;
   }
 
   updateState(newTime) {
     super.updateState(newTime);
-    // let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
-    this.D = this._constrainDispersion(this.D);
+    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 (${Pe_local}) is too high! Increase reactor resolution.`);
+    (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${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) {
@@ -324,26 +288,25 @@ class Reactor_PFR extends Reactor {
    * @returns {Array} - New reactor state.
    */
   tick(time_step) {
-    this._applyBoundaryConditions();
-
-    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
-    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));
+    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.state);
+    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 transfer = Array.from(Array(this.n_x), () => 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 = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+      for (let i = 1; i < this.n_x - 1; i++) {
         transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
       }
     } else {
-    for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
-        transfer[i][S_O_INDEX] = this._calcOTR(this.extendedState[i][S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
+    for (let i = 1; i < 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);
       }
     }
 
-    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
+    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
 
     const stateNew = math.add(this.state, dC_total);
+    this._applyBoundaryConditions(stateNew);
 
     if (DEBUG) {
       assertNoNaN(dispersion, "dispersion");
@@ -354,14 +317,13 @@ 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) {
     switch(measurementType) {
       case "quantity (oxygen)":
-        let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+        let grid_pos = Math.round(position / this.config.length * this.n_x);
         this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
         break;
       default:
@@ -373,51 +335,57 @@ 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() {
-    if (this.upstreamReactor) {
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
-      }
+  _applyBoundaryConditions(state) {
+    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])));
     } 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);
-        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);
-      }
+      state[0] = state[1];
     }
+    // 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() { // create gradient operator
-    const D_size = this.n_x+2*BC_PADDING;
-    const I = math.resize(math.diag(Array(D_size).fill(1/12), -2), [D_size, D_size]);
-    const A = math.resize(math.diag(Array(D_size).fill(-2/3), -1), [D_size, D_size]);
-    const B = math.resize(math.diag(Array(D_size).fill(2/3), 1), [D_size, D_size]);
-    const C = math.resize(math.diag(Array(D_size).fill(-1/12), 2), [D_size, D_size]);
-    const D = math.add(I, A, B, C);
-    // set by BCs elsewhere
-    D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
-    return D;
+  _makeDoperator(central = false, higher_order = false) { // create gradient operator
+    if (higher_order) {
+      if (central) {
+        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(this.n_x).fill(-2/3), -1), [this.n_x, this.n_x]);
+        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(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);
+        NearBoundary[0] = -1/4;
+        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;
+    }
   }
 
   /**
@@ -425,24 +393,14 @@ class Reactor_PFR extends Reactor {
    * @returns {Array} - Second derivative operator matrix.
    */
   _makeD2operator() { // create the central second derivative operator
-    const D_size = this.n_x+2*BC_PADDING;
-    const I = math.diag(Array(D_size).fill(-2), 0);
-    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 I = math.diag(Array(this.n_x).fill(-2), 0);
+    const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]);
+    const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]);
     const D2 = math.add(I, A, B);
-    // set by BCs elsewhere
-    D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
+    D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
+    D2[this.n_x - 1] = Array(this.n_x).fill(0);
     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 };