From cd3a19e66fdcad602b208073395aae57d4e1c060 Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 2 Oct 2025 13:48:47 +0200
Subject: [PATCH] Fix boundary conditions for advection

---
 src/specificClass.js | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/specificClass.js b/src/specificClass.js
index 9a7e41d..ac1487b 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -301,7 +301,7 @@ class Reactor_PFR extends Reactor {
 
     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.temperrature));
+    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
@@ -310,7 +310,7 @@ class Reactor_PFR extends Reactor {
       }
     } else {
     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);
       }
     }
 
@@ -347,6 +347,8 @@ class Reactor_PFR extends Reactor {
    *  for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
    */
   _applyBoundaryConditions() {
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+
     if (this.upstreamReactor) {
       for (let i = 0; i < BC_PADDING; i++) {
         this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
@@ -356,8 +358,11 @@ 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 = (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 {
-        this.extendedState[BC_PADDING] = this.extendedState[BC_PADDING+1];
+        for (let i = 0; i < BC_PADDING; i++) {
+          this.extendedState[i] = this.extendedState[BC_PADDING];
+        }
       }
     }
 
@@ -371,8 +376,6 @@ class Reactor_PFR extends Reactor {
         this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
       }
     }
-
-    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
   }
 
   /**