reactor/src/reactor_class.js

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
};

const math = create(all, config);

const S_O_INDEX = 0;
const NUM_SPECIES = 13;

class Reactor {
    /**
     * Reactor base class.
     * @param {object} config - Configuration object containing reactor parameters.
     */
    constructor(config) {
        this.asm = new ASM3();

        this.volume = config.volume; // fluid volume reactor [m3]

        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.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
    }

    /**
     * Setter for influent data.
     * @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
    */
    set setInfluent(input) {
        let index_in = input.payload.inlet;
        this.Fs[index_in] = input.payload.F;
        this.Cs_in[index_in] = input.payload.C;
        // DEBUG
        // 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));
    }

    /**
     * Setter for OTR (Oxygen Transfer Rate).
     * @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1].
     */
    set setOTR(input) {
        this.OTR = input.payload;
    }

    /**
     * 
     * @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
     * @param {number} T - Temperature in Celsius, default to 20 C.
     * @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;
        return this.kla * (S_O_sat - S_O);
    }

    /**
     * Clip values in an array to zero.
     * @param {Array} arr - Array of values to clip.
     * @returns {Array} - New array with values clipped to zero.
     */
    _arrayClip2Zero(arr) {
        if (Array.isArray(arr)) {
            return arr.map(x => this._arrayClip2Zero(x));
        } else {
            return arr < 0 ? 0 : arr;
        }
    }

    /**
     * Update the reactor state based on the new time.
     * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
     */
    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));
        if (n_iter) {
            let n = 0;
            while (n < n_iter) {
                this.tick(this.timeStep);
                n += 1;
            }
            this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor;
        }
    }

}

class Reactor_CSTR extends Reactor {
    /**
     * Reactor_CSTR class for Continuous Stirred Tank Reactor.
     * @param {object} config - Configuration object containing reactor parameters.
     */
    constructor(config) {
        super(config);
        this.state = config.initialState;
    }

    /**
     * Getter for effluent data.
     * @returns {object} Effluent data object (msg), defaults to inlet 0.
     */
    get getEffluent() { // getter for Effluent, defaults to inlet 0
        return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
    }

    /**
     * Tick the reactor state using the forward Euler method.
     * @param {number} time_step - Time step for the simulation [d].
     * @returns {Array} - New reactor state.
     */
    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 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

        const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step);
        assertNoNaN(dC_total, "change in state");

        this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
        assertNoNaN(this.state, "new state");
        return this.state;
    }
}

class Reactor_PFR extends Reactor {
    /**
     * Reactor_PFR class for Plug Flow Reactor.
     * @param {object} config - Configuration object containing reactor parameters.
     */
    constructor(config) {
        super(config);

        this.length = config.length; // reactor length [m]
        this.n_x = config.resolution_L; // number of slices

        this.d_x = this.length / this.n_x;
        this.A = this.volume / this.length; // crosssectional area [m2]

        this.state = Array.from(Array(this.n_x), () => config.initialState.slice())

        // console.log("Initial State: ")
        // console.log(this.state)

        this.D = 0.0; // axial dispersion [m2 d-1]

        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");
    }

    /**
     * Setter for axial dispersion.
     * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
     */
    set setDispersion(input) {
        this.D = input.payload;
    }

    /**
     * Getter for effluent data.
     * @returns {object} Effluent data object (msg), defaults to inlet 0.
     */
    get getEffluent() {
        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;
            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];
            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]
    }

    /**
     * Tick the reactor state using explicit finite difference method.
     * @param {number} time_step - Time step for the simulation [d].
     * @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 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));

        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[S_O_INDEX] = this.OTR; });
        } else {
            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);
        assertNoNaN(dC_total, "change in state");

        const stateNew = math.add(this.state, dC_total);
        assertNoNaN(stateNew, "new state");

        this._applyBoundaryConditions(stateNew);
        assertNoNaN(stateNew, "new state post BC");

        this.state = this._arrayClip2Zero(stateNew);
        return stateNew;
    }

    /**
     * Create finite difference first derivative operator.
     * @param {boolean} central - Use central difference scheme if true, otherwise use upwind scheme.
     * @param {boolean} higher_order - Use higher order scheme if true, otherwise use first order scheme.
     * @returns {Array} - First derivative operator matrix.
     */
    _makeDoperator(central = false, higher_order = false) { // create gradient operator
        if (higher_order) {
            if (central) {
                const I = math.resize(math.diag(Array(this.n_x).fill(1/12), -2), [this.n_x, this.n_x]);
                const A = math.resize(math.diag(Array(this.n_x).fill(-2/3), -1), [this.n_x, this.n_x]);
                const B = math.resize(math.diag(Array(this.n_x).fill(2/3), 1), [this.n_x, this.n_x]);
                const C = math.resize(math.diag(Array(this.n_x).fill(-1/12), 2), [this.n_x, this.n_x]);
                const D = math.add(I, A, B, C);
                const NearBoundary = Array(this.n_x).fill(0.0);
                NearBoundary[0] = -1/4;
                NearBoundary[1] = -5/6;
                NearBoundary[2] = 3/2;
                NearBoundary[3] = -1/2;
                NearBoundary[4] = 1/12;
                D[1] = NearBoundary;
                NearBoundary.reverse();
                D[this.n_x-2] = math.multiply(-1, NearBoundary);
                D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
                D[this.n_x-1] = Array(this.n_x).fill(0);
                return D;
            } else {
                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 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);
            return D;
        }
    }

    /**
     * Create central finite difference second derivative operator.
     * @returns {Array} - Second derivative operator matrix.
     */
    _makeD2operator() { // create the central second derivative operator
        const I = math.diag(Array(this.n_x).fill(-2), 0);
        const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]);
        const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]);
        const D2 = math.add(I, A, B);
        D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
        D2[this.n_x - 1] = Array(this.n_x).fill(0);
        return D2;
    }
}

module.exports = { Reactor_CSTR, Reactor_PFR };

// DEBUG
// state: 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
// let initial_state = [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];
// const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
// Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
// Reactor.Fs[0] = 10;
// Reactor.D = 0.01;
// let N = 0;
// while (N < 5000) {
//     console.log(Reactor.tick(0.001));
//     N += 1;
// }