Refactor advanced-reactor and nodeClass for improved readability and consistency

src/nodeClass.js

@@ -20,7 +20,6 @@ class nodeClass {
         this._setupClass();
 
         this._attachInputHandler();
-
     }
 
     /**

src/reactor_class.js

@@ -2,11 +2,16 @@ const ASM3 = require('./asm3_class.js')
 const { create, all } = require('mathjs')
 
 const config = {
-  matrix: 'Array' // choose 'Matrix' (default) or 'Array'
+    matrix: 'Array' // use Array as the matrix type
 }
 
 const math = create(all, config)
 
+/**
+ * Assert that no NaN values are present in an array.
+ * @param {Array} arr 
+ * @param {string} label 
+ */
 function assertNoNaN(arr, label = "array") {
     if (math.isNaN(arr)) {
         throw new Error("NaN detected in ${label}!");
@@ -133,7 +138,7 @@ class Reactor_CSTR extends Reactor {
 
         const dC_total = math.multiply(math.add(dC_in, dC_out, r, t_O), time_step);
 
-        this.state = this_.arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
+        this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
         return this.state;
     }
 }
@@ -179,6 +184,24 @@ class Reactor_PFR extends Reactor {
         return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
     }
 
+    _applyBoundaryConditions(newState) {
+        // apply boundary conditions
+        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_gradient = Array(this.n_x).fill(0.0);
+            BC_gradient[0] = -1;
+            BC_gradient[1] = 1;
+            let Pe = this.length * math.sum(this.Fs) / (this.D * this.A)
+            const BC_dispersion = math.multiply((1 - (1 + 4 * this.volume / math.sum(this.Fs) / Pe) ^ 0.5) / Pe, [BC_gradient], stateNew)[0];
+            newState[0] = math.add(BC_C_in, BC_dispersion).map(val => val < 0 ? 0 : val);
+        } else { // Neumann BC (no flux)
+            newState[0] = newState[1];
+        }
+        // Neumann BC (no flux)
+        newState[this.n_x - 1] = newState[this.n_x - 2]
+        return newState
+    }
+
     /**
      * Tick the reactor state using explicit finite difference method.
      * @param {number} time_step - Time step for the simulation [d].
@@ -201,30 +224,16 @@ class Reactor_PFR extends Reactor {
         }
 
         const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
-        const new_state = math.add(this.state, dC_total);
+        let stateNew = math.add(this.state, dC_total);
 
-        assertNoNaN(new_state, "new state");
+        assertNoNaN(stateNew, "new state");
 
-        // apply boundary conditions
+        stateNew = this._applyBoundaryConditions(stateNew);
-        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_gradient = Array(this.n_x).fill(0.0);
-            BC_gradient[0] = -1;
-            BC_gradient[1] = 1;
-            let Pe = this.length*math.sum(this.Fs)/(this.D*this.A)
-            const BC_dispersion = math.multiply((1-(1+4*this.volume/math.sum(this.Fs)/Pe)^0.5)/Pe, [BC_gradient], new_state)[0];
-            new_state[0] = math.add(BC_C_in, BC_dispersion).map(val => val < 0 ? 0 : val);
 
-        } else { // Neumann BC (no flux)
+        assertNoNaN(stateNew, "new state post BC");
-            new_state[0] = new_state[1];
-        }
-        // Neumann BC (no flux)
-        new_state[this.n_x-1] = new_state[this.n_x-2]
 
-        assertNoNaN(new_state, "new state post BC");
+        this.state = this._arrayClip2Zero(stateNew);
-
+        return stateNew;
-        this.state = this._arrayClip2Zero(new_state);
-        return new_state;
     }
 
     /**