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Merge pull request 'Switch temperature to Measurement node and finally fix boundary conditions properly' (#14) from experimental into main

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Reviewed-on: p.vanderwilt/asm3#14
This commit is contained in:
p.vanderwilt
2025-07-11 10:44:26 +00:00
parent 6bdfa07d92 6227bbe256
commit 6adf29427a
4 changed files with 290 additions and 257 deletions
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6
package-lock.json generated
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@@ -9,6 +9,7 @@
"version": "0.0.1",
"license": "SEE LICENSE",
"dependencies": {
"generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git",
"mathjs": "^14.5.2"
}
},
@@ -59,6 +60,11 @@
"url": "https://github.com/sponsors/rawify"
}
},
"node_modules/generalFunctions": {
"version": "1.0.0",
"resolved": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git#950ca2b6b4e91b37479aee90bff74b02c16f130e",
"license": "SEE LICENSE"
},
"node_modules/javascript-natural-sort": {
"version": "0.7.1",
"resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",

1
package.json
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@@ -27,6 +27,7 @@
}
},
"dependencies": {
"generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/p.vanderwilt/generalFunctions.git",
"mathjs": "^14.5.2"
}
}

9
src/nodeClass.js
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@@ -42,9 +42,18 @@ class nodeClass {
case "OTR":
this.reactor.setOTR = msg;
break;
case "Temperature":
this.reactor.setTemperature = msg;
break;
case "Dispersion":
this.reactor.setDispersion = msg;
break;
case 'registerChild':
// Register this node as a child of the parent node
const childId = msg.payload;
const childObj = this.RED.nodes.getNode(childId);
this.reactor.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
break;
default:
console.log("Unknown topic: " + msg.topic);
}

97
src/specificClass.js
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@@ -1,6 +1,7 @@
const ASM3 = require('./reaction_modules/asm3_class.js');
const { create, all } = require('mathjs');
const { assertNoNaN } = require('./utils.js');
const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
const config = {
matrix: 'Array' // use Array as the matrix type
@@ -10,7 +11,7 @@ const math = create(all, config);
const S_O_INDEX = 0;
const NUM_SPECIES = 13;
const DEBUG = true;
const DEBUG = false;
class Reactor {
/**
@@ -18,6 +19,11 @@ class Reactor {
* @param {object} config - Configuration object containing reactor parameters.
*/
constructor(config) {
// EVOLV stuff
this.logger = new logger(); //TODO: attach config
this.measurements = new MeasurementContainer();
this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
this.asm = new ASM3();
this.volume = config.volume; // fluid volume reactor [m3]
@@ -25,12 +31,25 @@ class Reactor {
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.temperature = 20; // temperature [C]
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.speedUpFactor = 1; // speed up factor for simulation, 60 means 1 minute per simulated second
this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
}
updateMeasurement(variant, subType, value, position) {
this.logger.debug(`---------------------- updating ${subType} ------------------ `);
switch (subType) {
case "temperature":
this.temperature = value;
break;
default:
this.logger.error(`Type '${subType}' not recognized for measured update.`);
return;
}
}
/**
@@ -92,7 +111,6 @@ class Reactor {
this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor;
}
}
}
class Reactor_CSTR extends Reactor {
@@ -121,9 +139,9 @@ class Reactor_CSTR extends Reactor {
tick(time_step) { // tick reactor state using forward Euler method
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 reaction = this.asm.compute_dC(this.state, this.temperature);
const transfer = Array(NUM_SPECIES).fill(0.0);
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
transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // 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)
this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
@@ -173,21 +191,6 @@ class Reactor_PFR extends Reactor {
this.D = input.payload;
}
/**
* Setter for influent data.
* @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
*/
set setInfluent(input) {
super.setInfluent = input;
if(DEBUG) {
console.log("Inlet state max " + math.max(this.state[0]))
console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A));
console.log("Pe local " + this.d_x*math.sum(this.Fs)/(this.D*this.A));
console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x));
console.log("Co D " + this.D*this.timeStep/(this.d_x*this.d_x));
}
}
/**
* Getter for effluent data.
* @returns {object} Effluent data object (msg), defaults to inlet 0.
@@ -196,25 +199,21 @@ 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) {
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);
BC_gradient[0] = -1;
BC_gradient[1] = 1;
const BC_dispersion = math.multiply((1 - this.alpha) * this.D*this.A / (math.sum(this.Fs) * this.d_x), [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];
updateState(newTime) {
super.updateState(newTime);
let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
(Pe_local >= 2) && console.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
(Co_D >= 0.5) && console.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
if(DEBUG) {
console.log("Inlet state max " + math.max(this.state[0]))
console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A));
console.log("Pe local " + Pe_local);
console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x));
console.log("Co D " + Co_D);
}
// Neumann BC (no flux)
state[this.n_x-1] = state[this.n_x-2]
}
/**
@@ -225,13 +224,13 @@ class Reactor_PFR extends Reactor {
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 reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice));
const reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
transfer.forEach((x) => { x[S_O_INDEX] = this.OTR; });
} else {
transfer.forEach((x, i) => { x[S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX]); });
transfer.forEach((x, i) => { x[S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX], this.temperature); });
}
const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
@@ -251,6 +250,24 @@ class Reactor_PFR extends Reactor {
return stateNew;
}
/**
* 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) {
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 = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
state[0] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, state[1])));
} else {
state[0] = state[1];
}
// Neumann BC (no flux)
state[this.n_x-1] = state[this.n_x-2];
}
/**
* Create finite difference first derivative operator.
* @param {boolean} central - Use central difference scheme if true, otherwise use upwind scheme.