diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..1170717 --- /dev/null +++ b/.gitignore @@ -0,0 +1,136 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +lerna-debug.log* +.pnpm-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# Snowpack dependency directory (https://snowpack.dev/) +web_modules/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Optional stylelint cache +.stylelintcache + +# Microbundle cache +.rpt2_cache/ +.rts2_cache_cjs/ +.rts2_cache_es/ +.rts2_cache_umd/ + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variable files +.env +.env.development.local +.env.test.local +.env.production.local +.env.local + +# parcel-bundler cache (https://parceljs.org/) +.cache +.parcel-cache + +# Next.js build output +.next +out + +# Nuxt.js build / generate output +.nuxt +dist + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and not Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# vuepress v2.x temp and cache directory +.temp +.cache + +# vitepress build output +**/.vitepress/dist + +# vitepress cache directory +**/.vitepress/cache + +# Docusaurus cache and generated files +.docusaurus + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# TernJS port file +.tern-port + +# Stores VSCode versions used for testing VSCode extensions +.vscode-test + +# yarn v2 +.yarn/cache +.yarn/unplugged +.yarn/build-state.yml +.yarn/install-state.gz +.pnp.* diff --git a/advanced-reactor.html b/advanced-reactor.html new file mode 100644 index 0000000..f6bedc9 --- /dev/null +++ b/advanced-reactor.html @@ -0,0 +1,26 @@ + + + + + diff --git a/advanced-reactor.js b/advanced-reactor.js new file mode 100644 index 0000000..1cd3e21 --- /dev/null +++ b/advanced-reactor.js @@ -0,0 +1,23 @@ +module.exports = function(RED) { + function reactor(config) { + RED.nodes.createNode(this, config); + var node = this; + + let name = config.name; + + const Reactor = require('./dependencies/reactor_class'); + + const reactor = new Reactor(Array(13).fill(0.001)); + + node.on('input', function(msg, send, done) { + if (msg.topic == "clock") { + reactor.updateState(msg); + } + + if (done) { + done(); + } + }); + } + RED.nodes.registerType("advanced-reactor", reactor); +}; diff --git a/dependencies/asm3_class.js b/dependencies/asm3_class.js new file mode 100644 index 0000000..9ad03d9 --- /dev/null +++ b/dependencies/asm3_class.js @@ -0,0 +1,130 @@ +const math = require('mathjs') + +class ASM3 { + + kin_params = { + // Kinetic parameters (20 C for now) + + // Hydrolysis + k_H: 3., // hydrolysis rate constant [g X_S g-1 X_H d-1] + K_X: 1., // hydrolysis saturation constant [g X_S g-1 X_H] + // Heterotrophs + k_STO: 5., // storage rate constant [g S_S g-1 X_H d-1] + nu_NO: 0.6, // anoxic reduction factor [-] + K_O: 0.2, // saturation constant S_0 [g O2 m-3] + K_NO: 0.5, // saturation constant S_NO [g NO3-N m-3] + K_S: 2., // saturation constant S_s [g COD m-3] + K_STO: 1., // saturation constant X_STO [g X_STO g-1 X_H] + mu_H_max: 2., // maximum specific growth rate [d-1] + K_NH: 0.01, // saturation constant S_NH3 [g NH3-N m-3] + K_HCO: 0.1, // saturation constant S_HCO [mole HCO3 m-3] + b_H_O: 0.2, // aerobic respiration rate [d-1] + b_H_NO: 0.1, // anoxic respiration rate [d-1] + b_STO_O: 0.2, // aerobic respitation rate X_STO [d-1] + b_STO_NO: 0.1, // anoxic respitation rate X_STO [d-1] + // Autotrophs + mu_A_max: 1.0, // maximum specific growth rate [d-1] + K_A_NH: 1., // saturation constant S_NH3 [g NH3-N m-3] + K_A_O: 0.5, // saturation constant S_0 [g O2 m-3] + K_A_HCO: 0.5, // saturation constant S_HCO [mole HCO3 m-3] + b_A_O: 0.15, // aerobic respiration rate [d-1] + b_A_NO: 0.05 // anoxic respiration rate [d-1] + } + + stoi_params = { + // Stoichiometric and composition parameters + + f_SI: 0., // fraction S_I from hydrolysis [g S_I g-1 X_S] + f_XI: 0.2, // fraction X_I from decomp X_H [g X_I g-1 X_H] + // Yields + Y_STO_O: 0.85, // aerobic yield X_STO per S_S [g X_STO g-1 S_S] + Y_STO_NO: 0.80, // anoxic yield X_STO per S_S [g X_STO g-1 S_S] + Y_H_O: 0.63, // aerobic yield X_H per X_STO [g X_H g-1 X_STO] + Y_H_NO: 0.54, // anoxic yield X_H per X_STO [g X_H g-1 X_STO] + Y_A: 0.24, // anoxic yield X_A per S_NO [g X_A g-1 NO3-N] + // Composition (COD via DoR) + i_CODN: -1.71, // COD content (DoR) [g COD g-1 N2-N] + i_CODNO: -4.57, // COD content (DoR) [g COD g-1 NO3-N] + // Composition (nitrogen) + i_NSI: 0.01, // nitrogen content S_I [g N g-1 S_I] + i_NSS: 0.03, // nitrogen content S_S [g N g-1 S_S] + i_NXI: 0.02, // nitrogen content X_I [g N g-1 X_I] + i_NXS: 0.04, // nitrogen content X_S [g N g-1 X_S] + i_NBM: 0.07, // nitrogen content X_H / X_A [g N g-1 X_H / X_A] + // Composition (TSS) + i_TSXI: 0.75, // TSS content X_I [g TS g-1 X_I] + i_TSXS: 0.75, // TSS content X_S [g TS g-1 X_S] + i_TSBM: 0.90, // TSS content X_H / X_A [g TS g-1 X_H / X_A] + i_TSSTO: 0.60, // TSS content X_STO (PHB based) [g TS g-1 X_STO] + // Composition (charge) + i_cNH: 1/14, // charge per S_NH [mole H+ g-1 NH3-N] + i_cNO: -1/14 // charge per S_NO [mole H+ g-1 NO3-N] + } + + constructor() { + this.stoi_matrix = this._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); + // 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 + stoi_matrix[0] = [0., f_SI, 1.-f_SI, i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI, 0., 0., (i_NXS-(1.-f_SI)*i_NSS-f_SI*i_NSI)*i_cNH, 0., -1., 0., 0., 0., -i_TSXS]; + stoi_matrix[1] = [-(1.-Y_STO_O), 0, -1., i_NSS, 0., 0., i_NSS*i_cNH, 0., 0., 0., Y_STO_O, 0., Y_STO_O*i_TSSTO]; + stoi_matrix[2] = [0., 0., -1., i_NSS, -(1.-Y_STO_NO)/(i_CODNO-i_CODN), (1.-Y_STO_NO)/(i_CODNO-i_CODN), i_NSS*i_cNH + (1.-Y_STO_NO)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., Y_STO_NO, 0., Y_STO_NO*i_TSSTO]; + stoi_matrix[3] = [-(1.-Y_H_O)/Y_H_O, 0., 0., -i_NBM, 0., 0., -i_NBM*i_cNH, 0., 0., 1., -1./Y_H_O, 0., i_TSBM-i_TSSTO/Y_H_O]; + stoi_matrix[4] = [0., 0., 0., -i_NBM, -(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), (1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN)), -i_NBM*i_cNH+(1.-Y_H_NO)/(Y_H_NO*(i_CODNO-i_CODN))*i_cNO, 0., 0., 1., -1./Y_H_NO, 0., i_TSBM-i_TSSTO/Y_H_NO]; + stoi_matrix[5] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; + stoi_matrix[6] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, f_XI, 0., -1., 0., 0., f_XI*i_TSXI-i_TSBM]; + stoi_matrix[7] = [-1., 0., 0., 0., 0., 0., 0., 0., 0., 0., -1., 0., -i_TSSTO]; + stoi_matrix[8] = [0., 0., 0., 0., -1./(i_CODNO-i_CODN), 1./(i_CODNO-i_CODN), i_cNO/(i_CODNO-i_CODN), 0., 0., 0., -1., 0., -i_TSSTO]; + stoi_matrix[9] = [1.+i_CODNO/Y_A, 0., 0., -1./Y_A-i_NBM, 0., 1./Y_A, (-1./Y_A-i_NBM)*i_cNH+i_cNO/Y_A, 0., 0., 0., 0., 1., i_TSBM]; + stoi_matrix[10] = [f_XI-1., 0., 0., i_NBM-f_XI*i_NXI, 0., 0., (i_NBM-f_XI*i_NXI)*i_cNH, f_XI, 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; + stoi_matrix[11] = [0., 0., 0., i_NBM-f_XI*i_NXI, -(1.-f_XI)/(i_CODNO-i_CODN), (1.-f_XI)/(i_CODNO-i_CODN), (i_NBM-f_XI*i_NXI)*i_cNH+(1-f_XI)/(i_CODNO-i_CODN)*i_cNO, 0., 0., 0., 0., -1., f_XI*i_TSXI-i_TSBM]; + + return stoi_matrix[0].map((col, i) => stoi_matrix.map(row => row[i])); // transpose matrix + } + + _monod(c, K){ + return c / (K + c); + } + + _inv_monod(c, K){ + return K / (K + c); + } + + compute_rates(state) { // computes reaction rates. state is optional + // 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 + 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] = 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 + rates[0] = k_H * this._monod(X_S / X_H, K_X) * X_H; + + // Heterotrophs + rates[1] = k_STO * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H; + rates[2] = k_STO * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_S, K_S) * X_H; + rates[3] = mu_H_max * this._monod(S_O, K_O) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; + rates[4] = mu_H_max * nu_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * this._monod(S_NH, K_NH) * this._monod(S_HCO, K_HCO) * this._monod(X_STO/X_H, K_STO) * X_H; + rates[5] = b_H_O * this._monod(S_O, K_O) * X_H; + rates[6] = b_H_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H; + rates[7] = b_STO_O * this._monod(S_O, K_O) * X_H; + rates[8] = b_STO_NO * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO; + + // Autotrophs + rates[9] = mu_A_max * this._monod(S_O, K_A_O) * this._monod(S_NH, K_A_NH) * this._monod(S_HCO, K_A_HCO) * X_A; + rates[10] = b_A_O * this._monod(S_O, K_O) * X_A; + rates[11] = b_A_NO * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A; + + return rates; + } + + compute_dC(state) { // compute changes in concentrations + // 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 + return math.multiply(this.stoi_matrix, this.compute_rates(state)); + } +} + +module.exports = ASM3; \ No newline at end of file diff --git a/dependencies/reactor_class.js b/dependencies/reactor_class.js new file mode 100644 index 0000000..8c69516 --- /dev/null +++ b/dependencies/reactor_class.js @@ -0,0 +1,63 @@ +const ASM3 = require('./asm3_class') +const math = require('mathjs') + +class Reactor_CSTR { + + constructor(initial_state) { + this.state = initial_state; + console.log(this.state); + this.asm = new ASM3(); + + this.Vl = 10.0; // fluid volume reactor [m3] + this.F = 1.0; // fluid debit [m3 d-1] + this.C_in = [0., 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.]; // composition influent + this.OTR = 100.0; // oxygen transfer rate [g O2 d-1] + + this.currentTime = Date.now(); // milliseconds since epoch [ms] + this.timeStep = 1/(24*60*15) // time step [d] + } + + // expect update with timestamp + updateState(input) { + let newTime = input.payload; + + const day2ms = 1000 * 60 * 60 * 24; + + let n_iter = Math.floor((newTime - this.currentTime) / (this.timeStep * day2ms)); + if (n_iter > 0) { + let n = 0; + while (n < n_iter) { + console.log(this.tick_fe(this.timeStep)); + n += 1; + } + this.currentTime += n_iter * this.timeStep * day2ms; + n_iter = 0; + } + } + + tick_fe(time_step) { // tick reactor state using forward Euler method + const r = this.asm.compute_dC(this.state); + const dC_in = math.multiply(this.C_in, this.F/this.Vl); + const dC_out = math.multiply(this.state, this.F/this.Vl); + const T_O = Array(13).fill(0.0); + T_O[0] = this.OTR; + + const dC_total = math.multiply(math.add(dC_in, dC_out, r, T_O), time_step); + + this.state = math.add(this.state, dC_total); + return this.state; + } +} + +// testing stuff +// 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_CSTR(initial_state); +// Reactor.C_in = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.]; +// N = 0; +// while (N < 500) { +// console.log(Reactor.tick_fe(0.001)); +// N += 1; +// } + +module.exports = Reactor_CSTR; \ No newline at end of file diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 0000000..e2e89fc --- /dev/null +++ b/package-lock.json @@ -0,0 +1,113 @@ +{ + "name": "asm3", + "version": "0.0.1", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "asm3", + "version": "0.0.1", + "license": "SEE LICENSE", + "dependencies": { + "mathjs": "^14.5.2" + } + }, 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"SEE LICENSE", + "author": "P.R. van der Wilt", + "main": "advanced-reactor.js", + "scripts": { + "test": "node advanced-reactor.js" + }, + "node-red": { + "nodes": { + "advanced-reactor": "advanced-reactor.js" + } + }, + "dependencies": { + "mathjs": "^14.5.2" + } +}