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Refactor reactor class to improve NaN handling and add utility function for NaN assertions

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p.vanderwilt
2025-07-04 16:28:35 +02:00
parent 6755f2bd28
commit a2cfb20e2c
2 changed files with 48 additions and 41 deletions
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71
src/reactor_class.js
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@@ -1,5 +1,6 @@
const ASM3 = require('./asm3_class.js');
const { create, all } = require('mathjs');
const { assertNoNaN } = require('./utils.js');
const config = {
matrix: 'Array' // use Array as the matrix type
@@ -7,26 +8,9 @@ const config = {
const math = create(all, config);
const OXYGEN_INDEX = 0;
const S_O_INDEX = 0;
const NUM_SPECIES = 13;
/**
* Assert that no NaN values are present in an array.
* @param {Array} arr
* @param {string} label
*/
function assertNoNaN(arr, label = "array") {
if (Array.isArray(arr)) {
for (const el of arr) {
assertNoNaN(el, label);
}
} else {
if (Number.isNaN(arr)) {
throw new Error(`NaN detected in ${label}!`);
}
}
}
class Reactor {
/**
* Reactor base class.
@@ -35,16 +19,16 @@ class Reactor {
constructor(config) {
this.asm = new ASM3();
this.Vl = config.volume; // fluid volume reactor [m3]
this.volume = config.volume; // fluid volume reactor [m3]
this.Fs = Array(config.n_inlets).fill(0.0); // fluid debits per inlet [m3 d-1]
this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0.0)); // composition influents
this.Fs = Array(config.n_inlets).fill(0); // fluid debits per inlet [m3 d-1]
this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0)); // composition influents
this.OTR = 0.0; // oxygen transfer rate [g O2 d-1]
this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
this.currentTime = Date.now(); // milliseconds since epoch [ms]
this.timeStep = 1 / (24 * 60 * 15); // time step [d]
this.timeStep = 1 / (24*60*15); // time step [d]
this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
}
@@ -78,7 +62,7 @@ class Reactor {
* @returns
*/
_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;
let 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);
}
@@ -102,7 +86,7 @@ class Reactor {
updateState(newTime) { // expect update with timestamp
const day2ms = 1000 * 60 * 60 * 24;
let n_iter = Math.floor(this.speedUpFactor * (newTime - this.currentTime) / (this.timeStep * day2ms));
let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms));
if (n_iter) {
let n = 0;
while (n < n_iter) {
@@ -139,11 +123,11 @@ class Reactor_CSTR extends Reactor {
* @returns {Array} - New reactor state.
*/
tick(time_step) { // tick reactor state using forward Euler method
const inflow = math.multiply(math.divide([this.Fs], this.Vl), this.Cs_in)[0];
const outflow = math.multiply(-1 * math.sum(this.Fs) / this.Vl, this.state);
const inflow = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
const reaction = this.asm.compute_dC(this.state);
const transfer = Array(NUM_SPECIES).fill(0.0);
transfer[OXYGEN_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[OXYGEN_INDEX]); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX]); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step);
assertNoNaN(dC_total, "change in state");
@@ -166,7 +150,7 @@ class Reactor_PFR extends Reactor {
this.n_x = config.resolution_L; // number of slices
this.d_x = this.length / this.n_x;
this.A = this.Vl / this.length; // crosssectional area [m2]
this.A = this.volume / this.length; // crosssectional area [m2]
this.state = Array.from(Array(this.n_x), () => config.initialState.slice())
@@ -177,7 +161,7 @@ class Reactor_PFR extends Reactor {
this.D_op = this._makeDoperator(true, true);
assertNoNaN(this.D_op, "Derivative operator");
this.D2_op = this._makeD2operator();
assertNoNaN(this.D2_op, "Second derivative operator");
}
@@ -198,21 +182,26 @@ class Reactor_PFR extends Reactor {
return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
}
/**
* Apply boundary conditions to the reactor state.
* for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux
* for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
* @param {Array} state - Current reactor state without enforced BCs.
*/
_applyBoundaryConditions(state) {
// 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);
const BC_gradient = Array(this.n_x).fill(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], state)[0];
const BC_dispersion = math.multiply((1 - (1 + 4*this.volume/math.sum(this.Fs)/Pe)^0.5) / Pe, [BC_gradient], state)[0];
state[0] = math.add(BC_C_in, BC_dispersion).map(val => val < 0 ? 0 : val);
} else { // Neumann BC (no flux)
state[0] = state[1];
}
// Neumann BC (no flux)
state[this.n_x - 1] = state[this.n_x - 2]
state[this.n_x-1] = state[this.n_x-2]
}
/**
@@ -221,19 +210,19 @@ class Reactor_PFR extends Reactor {
* @returns {Array} - New reactor state.
*/
tick(time_step) {
const dispersion = math.multiply(this.D / (this.d_x * this.d_x), this.D2_op, this.state);
const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A * this.d_x), this.D_op, this.state);
const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.state);
const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.state);
const reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice));
const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0.0));
const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
assertNoNaN(dispersion, "dispersion");
assertNoNaN(advection, "advection");
assertNoNaN(reaction, "reaction");
if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
transfer.forEach((x) => { x[OXYGEN_INDEX] = this.OTR; });
transfer.forEach((x) => { x[S_O_INDEX] = this.OTR; });
} else {
transfer.forEach((x, i) => { x[OXYGEN_INDEX] = this._calcOTR(this.state[i][OXYGEN_INDEX]); });
transfer.forEach((x, i) => { x[S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX]); });
}
const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
@@ -279,11 +268,11 @@ class Reactor_PFR extends Reactor {
throw new Error("Upwind higher order method not implemented! Use central scheme instead.");
}
} else {
const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1 + central)), central), [this.n_x, this.n_x]);
const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1 + central)), -1), [this.n_x, this.n_x]);
const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1+central)), central), [this.n_x, this.n_x]);
const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1+central)), -1), [this.n_x, this.n_x]);
const D = math.add(I, A);
D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
D[this.n_x - 1] = Array(this.n_x).fill(0);
D[this.n_x-1] = Array(this.n_x).fill(0);
return D;
}
}

18
src/utils.js Normal file
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@@ -0,0 +1,18 @@
/**
* Assert that no NaN values are present in an array.
* @param {Array} arr
* @param {string} label
*/
function assertNoNaN(arr, label = "array") {
if (Array.isArray(arr)) {
for (const el of arr) {
assertNoNaN(el, label);
}
} else {
if (Number.isNaN(arr)) {
throw new Error(`NaN detected in ${label}!`);
}
}
}
module.exports = { assertNoNaN };