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Add optional state parameter to compute_rates, improve comments, and implement compute_dC method

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p.vanderwilt
2025-06-05 17:23:51 +02:00
parent f9bd4279aa
commit 333efcda52
1 changed files with 12 additions and 4 deletions
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16
dependencies/asm3_class.js vendored
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@@ -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())
console.log(asm3.compute_rates())
console.log(asm3.compute_dC(0.001))