Minor fixes

reactor.html

@@ -31,7 +31,7 @@
             enableLog: { value: false },
             logLevel: { value: "error" },
 
-            positionVsParent: { value: "" },
+            positionVsParent: { value: "" }
         },
         inputs: 1,
         outputs: 3,

src/reaction_modules/asm3_class Koch.js

@@ -2,6 +2,8 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 

src/reaction_modules/asm3_class.js

@@ -2,6 +2,8 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 

src/specificClass.js

@@ -203,7 +203,7 @@ class Reactor {
    * Update the reactor state based on the new time.
    * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
    */
-  updateState(newTime = Date.now()) { // expect update with timestamp
+  updateState(newTime) { // expect update with timestamp
     if (this.upstreamReactor) {
       this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
     }
@@ -326,8 +326,8 @@ class Reactor_PFR extends Reactor {
         transfer[i][ASM_CONSTANTS.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++) {
+      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
-        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
+        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature);
       }
     }
 
@@ -349,10 +349,19 @@ class Reactor_PFR extends Reactor {
   }
 
   _updateMeasurement(measurementType, value, position, context) {
+    const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+
+    // naive approach for reconciling measurements and simulation
+    // could benefit from Kalman filter?
     switch(measurementType) {
       case "quantity (oxygen)":
-        const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+        this.state[grid_pos][ASM_CONSTANTS.S_O_INDEX] = value;
-        this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
+        break;
+      case "quantity (ammonium)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NH_INDEX] = value;
+        break;
+      case "quantity (nox)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NO_INDEX] = value;
         break;
       default:
         super._updateMeasurement(measurementType, value, position, context);
@@ -375,6 +384,7 @@ class Reactor_PFR extends Reactor {
         const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
         const BC_dispersion_term = 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])));
+        // Numerical boundary condition
         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 {
         // Neumann BC (no flux)