From 260d04b96f3b3d477138c0e8425547bad4ba2c1e Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 16:36:51 +0100
Subject: [PATCH] Minor optimisations in code and clarification

---
 src/specificClass.js | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/specificClass.js b/src/specificClass.js
index 793f741..228d077 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -1,5 +1,5 @@
 const { ASM3, ASM_CONSTANTS } = require('./reaction_modules/asm3_class.js');
-const { create, all, isArray, i } = require('mathjs');
+const { create, all, isArray } = require('mathjs');
 const { assertNoNaN } = require('./utils.js');
 const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
 const EventEmitter = require('events');
@@ -96,7 +96,7 @@ class Reactor {
    * @returns {number} - Calculated OTR [g O2 d-1 m-3].
    */
   _calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C
-    let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
+    const S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
     return this.kla * (S_O_sat - S_O);
   }
 
@@ -208,7 +208,7 @@ class Reactor {
       this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
     }
 
-    let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
+    const n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
     if (n_iter) {
       let n = 0;
       while (n < n_iter) {
@@ -294,7 +294,7 @@ class Reactor_PFR extends Reactor {
     super.updateState(newTime);
     // 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);
+    const Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
 
     // (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
     (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
@@ -351,7 +351,7 @@ class Reactor_PFR extends Reactor {
   _updateMeasurement(measurementType, value, position, context) {
     switch(measurementType) {
       case "quantity (oxygen)":
-        let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+        const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
         this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
         break;
       default:
@@ -366,31 +366,31 @@ class Reactor_PFR extends Reactor {
    */
   _applyBoundaryConditions() {
     if (this.upstreamReactor) {
+      // Open boundary
       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
+      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 = 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];
-        }
+        // Neumann BC (no flux)
+        this.extendedState.fill(this.extendedState[BC_PADDING], 0, BC_PADDING);
       }
     }
 
     if (this.downstreamReactor) {
+      // Open boundary
       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);
-      }
+      this.extendedState.fill(this.extendedState.at(-1-BC_PADDING), BC_PADDING+this.n_x);
     }
   }