From 333efcda5299d9520e7d68baedfed0fda6092bba Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 5 Jun 2025 17:23:51 +0200
Subject: [PATCH] Add optional state parameter to compute_rates, improve
 comments, and implement compute_dC method

---
 dependencies/asm3_class.js | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/dependencies/asm3_class.js b/dependencies/asm3_class.js
index 6aea036..1cf4ec0 100644
--- a/dependencies/asm3_class.js
+++ b/dependencies/asm3_class.js
@@ -1,3 +1,5 @@
+const math = require('mathjs')
+
 class ASM3 {
 
   kin_params = {
@@ -65,7 +67,7 @@ class ASM3 {
     this.stoi_matrix = this._initialise_stoi_matrix()
   }
 
-  _initialise_stoi_matrix(){
+  _initialise_stoi_matrix(){ // initialise stoichiometric matrix
     const { f_SI, f_XI, Y_STO_O, Y_STO_NO, Y_H_O, Y_H_NO, Y_A, i_CODN, i_CODNO, i_NSI, i_NSS, i_NXI, i_NXS, i_NBM, i_TSXI, i_TSXS, i_TSBM, i_TSSTO, i_cNH, i_cNO } = this.stoi_params;
 
     const stoi_matrix = Array(12);
@@ -94,9 +96,10 @@ class ASM3 {
     return K / (K + c);
   }
 
-  compute_rates() {
+  compute_rates(state) { // computes reaction rates. state is optional, if not provided, use class state
+
     const rates = Array(12);
-    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = this.state;
+    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state || this.state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     
     // Hydrolysis
@@ -119,8 +122,13 @@ class ASM3 {
 
     return rates;
   }
+
+  compute_dC(dt){ // compute change in concentration over time step dt
+    return math.multiply(math.multiply(this.stoi_matrix, this.compute_rates()), dt);
+  }
 }
 
 // testing stuff
 const asm3 = new ASM3([0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1])
-console.log(asm3.compute_rates())
\ No newline at end of file
+console.log(asm3.compute_rates())
+console.log(asm3.compute_dC(0.001))
\ No newline at end of file