Add example flow

Shift fields around in node parameters
Update README.md
2025-11-28 14:29:53 +01:00 · 2025-11-28 11:52:40 +01:00 · 2025-11-28 10:51:10 +00:00 · 2025-11-21 13:48:18 +00:00 · 2025-11-21 12:29:46 +01:00 · 2025-11-21 11:02:40 +01:00
11 changed files with 2399 additions and 15 deletions
--- a/.gitignore
+++ 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
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+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
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+build/Release
+
+# Dependency directories
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+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
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+.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
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+
+# Next.js build output
+.next
+out
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+# Nuxt.js build / generate output
+.nuxt
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+# 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
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+# vuepress build output
+.vuepress/dist
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+.temp
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+.dynamodb/
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+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
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+.yarn/build-state.yml
+.yarn/install-state.gz
+.pnp.*
--- a/README.md
+++ b/README.md
@@ -1,16 +1,20 @@
-# reactor
+# Reactor: Advanced Hydraulic Tank & Biological Process Simulator

-Reactor: Advanced Hydraulic Tank & Biological Process Simulator
+A comprehensive reactor class for wastewater treatment simulation featuring non-ideal plug flow hydraulics and ASM3 biological modeling.

-A comprehensive reactor class for wastewater treatment simulation featuring plug flow hydraulics, ASM1-ASM3 biological modeling, and multi-sectional concentration tracking. Implements hydraulic retention time calculations, dispersion modeling, and real-time biological reaction kinetics for accurate process simulation.
+## How to use this Node
+### Set Node Properties
+- Set reactor type: Continuously Stirred Tank Reactor (CSTR) or Plug Flow Reactor (PFR)
+- Configure reactor sizing: Set reactor volume [ $m^3$ ] and (for PFRs) set the reactor length [ $m$ ]
+- (For PFRs) set reactor spatial resolution: A value of 10 or 20 is good. A higher resolution means more accurate simulation, at higher computational expense. Note that connected reactors must have similar Δx values.
+- Set initial state of reactor: set the intial concentrations of all relevant reaction species.
+- (Optional) set $k_L a$ to calculate OTR internally, rather than providing it explicitly, using simple mass transfer model.

-Key Features:
+### Accepted Node inputs
+- \{ topic: clock, payload: \<timestamp [ $ms$ ]\> \} - **required** clock signal to make reactor update state.
+- \{ topic: Fluent, payload: \{ F: \<flow rate [ $m^3 d^{-1}$ ]\>, C: \<array with concentrations\> \} \} - sets inflow composition and flow rate.
+- \{ topic: Dispersion, payload: \<dispersion coefficient in [ $m d^{-2}$ ]\> \} - sets PFR dispersion coefficient.
+- \{ topic: OTR, payload: \<oxygen transfer rate [ $ g d^{-1} m^{-3}$ ]\> \} - sets current oxygen transfer rate.

-Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
-ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
-Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
-Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves
-Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
-Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
-Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
-Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.
+## Troubleshooting
+Check for possible numerical warnings. These tell you which simulation parameters to change. If solutions appear to be oscillate, try reducing the time step. If solutions appear to be too dispersive, try increasing the reactor resolution.
--- a/example_flow/reactor_flows.json
+++ b/example_flow/reactor_flows.json
@@ -0,0 +1,838 @@
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+        "func": "if (msg.topic != \"Fluent\" || msg.payload.inlet == 0) {\n    return;\n}\n\nconst [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] = msg.payload.C;\n\nmsg = {payload: [\n    { \"Series\": \"X_I\",      \"Y\": X_I},\n    { \"Series\": \"X_S\",      \"Y\": X_S},\n    { \"Series\": \"X_H\",      \"Y\": X_H},\n    { \"Series\": \"X_STO\",    \"Y\": X_STO},\n    { \"Series\": \"X_A\",      \"Y\": X_A},\n    { \"Series\": \"X_TS\",     \"Y\": X_TS}\n    ]};\n\nreturn msg;",
+        "outputs": 1,
+        "timeout": 0,
+        "noerr": 0,
+        "initialize": "",
+        "finalize": "",
+        "libs": [],
+        "x": 1320,
+        "y": 380,
+        "wires": [
+            [
+                "0a3ffa69046a4844"
+            ]
+        ]
+    },
+    {
+        "id": "0a3ffa69046a4844",
+        "type": "ui-chart",
+        "z": "a6b85e226d144df1",
+        "group": "de8b029d69f26c0e",
+        "name": "Sludge composition",
+        "label": "Sludge composition",
+        "order": 9007199254740991,
+        "chartType": "line",
+        "category": "Series",
+        "categoryType": "property",
+        "xAxisLabel": "",
+        "xAxisProperty": "",
+        "xAxisPropertyType": "timestamp",
+        "xAxisType": "time",
+        "xAxisFormat": "",
+        "xAxisFormatType": "auto",
+        "xmin": "",
+        "xmax": "",
+        "yAxisLabel": "",
+        "yAxisProperty": "Y",
+        "yAxisPropertyType": "property",
+        "ymin": "",
+        "ymax": "",
+        "bins": 10,
+        "action": "append",
+        "stackSeries": false,
+        "pointShape": "circle",
+        "pointRadius": 4,
+        "showLegend": true,
+        "removeOlder": "8",
+        "removeOlderUnit": "3600",
+        "removeOlderPoints": "2000",
+        "colors": [
+            "#0095ff",
+            "#ff0000",
+            "#ff7f0e",
+            "#2ca02c",
+            "#a347e1",
+            "#d62728",
+            "#ff9896",
+            "#9467bd",
+            "#c5b0d5"
+        ],
+        "textColor": [
+            "#666666"
+        ],
+        "textColorDefault": true,
+        "gridColor": [
+            "#e5e5e5"
+        ],
+        "gridColorDefault": true,
+        "width": 6,
+        "height": 8,
+        "className": "",
+        "interpolation": "linear",
+        "x": 1530,
+        "y": 380,
+        "wires": [
+            []
+        ]
+    },
+    {
+        "id": "272b4b0050479d13",
+        "type": "measurement",
+        "z": "a6b85e226d144df1",
+        "name": "sensor",
+        "scaling": false,
+        "i_min": 0,
+        "i_max": 0,
+        "i_offset": 0,
+        "o_min": 3200,
+        "o_max": 4000,
+        "simulator": true,
+        "smooth_method": "",
+        "count": 10,
+        "uuid": "",
+        "supplier": "Vega",
+        "category": "Sensor",
+        "assetType": "Quantity (TSS)",
+        "model": "VegaSolidsProbe",
+        "unit": "g/m³",
+        "enableLog": true,
+        "logLevel": "error",
+        "positionVsParent": "atEquipment",
+        "positionIcon": "⊥",
+        "hasDistance": false,
+        "distance": "",
+        "x": 930,
+        "y": 580,
+        "wires": [
+            [],
+            [],
+            [
+                "47120bc82aa7bf49"
+            ]
+        ]
+    },
+    {
+        "id": "6baffb7954cf0cce",
+        "type": "function",
+        "z": "a6b85e226d144df1",
+        "name": "Data_converter",
+        "func": "if (msg.topic != \"Fluent\" || msg.payload.inlet == 1 || msg.payload.inlet == 2) {\n    return;\n}\n\nconst [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] = msg.payload.C;\n\nmsg = {payload: [\n    { \"Series\": \"S_O\",      \"Y\": S_O},\n    { \"Series\": \"S_I\",      \"Y\": S_I},\n    { \"Series\": \"S_S\",      \"Y\": S_S},\n    { \"Series\": \"S_NH\",     \"Y\": S_NH},\n    { \"Series\": \"S_N2\",     \"Y\": S_N2},\n    { \"Series\": \"S_NO\",     \"Y\": S_NO},\n    { \"Series\": \"S_HCO\",    \"Y\": S_HCO}\n    ]};\n\nreturn msg;",
+        "outputs": 1,
+        "timeout": 0,
+        "noerr": 0,
+        "initialize": "",
+        "finalize": "",
+        "libs": [],
+        "x": 1320,
+        "y": 420,
+        "wires": [
+            [
+                "df288814a2a9a2b1"
+            ]
+        ]
+    },
+    {
+        "id": "df288814a2a9a2b1",
+        "type": "ui-chart",
+        "z": "a6b85e226d144df1",
+        "group": "de8b029d69f26c0e",
+        "name": "Effluent",
+        "label": "Effluent",
+        "order": 9007199254740991,
+        "chartType": "line",
+        "category": "Series",
+        "categoryType": "property",
+        "xAxisLabel": "",
+        "xAxisProperty": "",
+        "xAxisPropertyType": "timestamp",
+        "xAxisType": "time",
+        "xAxisFormat": "",
+        "xAxisFormatType": "auto",
+        "xmin": "",
+        "xmax": "",
+        "yAxisLabel": "",
+        "yAxisProperty": "Y",
+        "yAxisPropertyType": "property",
+        "ymin": "",
+        "ymax": "",
+        "bins": 10,
+        "action": "append",
+        "stackSeries": false,
+        "pointShape": "circle",
+        "pointRadius": 4,
+        "showLegend": true,
+        "removeOlder": "8",
+        "removeOlderUnit": "3600",
+        "removeOlderPoints": "2000",
+        "colors": [
+            "#0095ff",
+            "#ff0000",
+            "#ff7f0e",
+            "#2ca02c",
+            "#a347e1",
+            "#d62728",
+            "#ff9896",
+            "#9467bd",
+            "#c5b0d5"
+        ],
+        "textColor": [
+            "#666666"
+        ],
+        "textColorDefault": true,
+        "gridColor": [
+            "#e5e5e5"
+        ],
+        "gridColorDefault": true,
+        "width": 6,
+        "height": 8,
+        "className": "",
+        "interpolation": "linear",
+        "x": 1520,
+        "y": 420,
+        "wires": [
+            []
+        ]
+    },
+    {
+        "id": "ae38454098a37db0",
+        "type": "ui-group",
+        "name": "Group 3",
+        "page": "ca564642bfc5606c",
+        "width": 6,
+        "height": 1,
+        "order": -1,
+        "showTitle": true,
+        "className": "",
+        "visible": "true",
+        "disabled": "false",
+        "groupType": "default"
+    },
+    {
+        "id": "de8b029d69f26c0e",
+        "type": "ui-group",
+        "name": "Group 4",
+        "page": "ca564642bfc5606c",
+        "width": 6,
+        "height": 1,
+        "order": -1,
+        "showTitle": true,
+        "className": "",
+        "visible": "true",
+        "disabled": "false",
+        "groupType": "default"
+    },
+    {
+        "id": "ca564642bfc5606c",
+        "type": "ui-page",
+        "name": "PFR",
+        "ui": "90eb5f47d95b4087",
+        "path": "/page2",
+        "icon": "home",
+        "layout": "grid",
+        "theme": "2c8bcaa0046b4323",
+        "breakpoints": [
+            {
+                "name": "Default",
+                "px": "0",
+                "cols": "3"
+            },
+            {
+                "name": "Tablet",
+                "px": "576",
+                "cols": "6"
+            },
+            {
+                "name": "Small Desktop",
+                "px": "768",
+                "cols": "9"
+            },
+            {
+                "name": "Desktop",
+                "px": "1024",
+                "cols": "12"
+            }
+        ],
+        "order": -1,
+        "className": "",
+        "visible": "true",
+        "disabled": "false"
+    },
+    {
+        "id": "90eb5f47d95b4087",
+        "type": "ui-base",
+        "name": "Dashboard",
+        "path": "/dashboard",
+        "appIcon": "",
+        "includeClientData": true,
+        "acceptsClientConfig": [
+            "ui-notification",
+            "ui-control"
+        ],
+        "showPathInSidebar": false,
+        "headerContent": "page",
+        "navigationStyle": "default",
+        "titleBarStyle": "default",
+        "showReconnectNotification": true,
+        "notificationDisplayTime": 1,
+        "showDisconnectNotification": true,
+        "allowInstall": true
+    },
+    {
+        "id": "2c8bcaa0046b4323",
+        "type": "ui-theme",
+        "name": "Default",
+        "colors": {
+            "surface": "#ffffff",
+            "primary": "#0094ce",
+            "bgPage": "#eeeeee",
+            "groupBg": "#ffffff",
+            "groupOutline": "#cccccc"
+        },
+        "sizes": {
+            "density": "default",
+            "pagePadding": "12px",
+            "groupGap": "12px",
+            "groupBorderRadius": "4px",
+            "widgetGap": "12px"
+        }
+    }
+]
--- a/package.json
+++ b/package.json
@@ -0,0 +1,32 @@
+{
+  "name": "reactor",
+  "version": "0.0.1",
+  "description": "Implementation of the asm3 model for Node-Red",
+  "repository": {
+    "type": "git",
+    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
+  },
+  "keywords": [
+    "asm3",
+    "activated sludge",
+    "wastewater",
+    "biological model",
+    "EVOLV",
+    "node-red"
+  ],
+  "license": "SEE LICENSE",
+  "author": "P.R. van der Wilt",
+  "main": "reactor.js",
+  "scripts": {
+    "test": "node reactor.js"
+  },
+  "node-red": {
+    "nodes": {
+      "reactor": "reactor.js"
+    }
+  },
+  "dependencies": {
+    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
+    "mathjs": "^14.5.2"
+  }
+}
--- a/reactor.html
+++ b/reactor.html
@@ -0,0 +1,239 @@
+<script src="/reactor/menu.js"></script>
+
+<script type="text/javascript">
+    RED.nodes.registerType("reactor", {
+        category: "EVOLV",
+        color: "#c4cce0",
+        defaults: {
+            name: { value: "" },
+            reactor_type: { value: "CSTR", required: true },
+            volume: { value: 0., required: true },
+            length: { value: 0.},
+            resolution_L: { value: 0.},
+            kla: { value: null },
+            
+            S_O_init: { value: 0., required: true },
+            S_I_init: { value: 30., required: true },
+            S_S_init: { value: 100., required: true },
+            S_NH_init: { value: 16., required: true },
+            S_N2_init: { value: 0., required: true },
+            S_NO_init: { value: 0., required: true },
+            S_HCO_init: { value: 5., required: true },
+            X_I_init: { value: 25., required: true },
+            X_S_init: { value: 75., required: true },
+            X_H_init: { value: 30., required: true },
+            X_STO_init: { value: 0., required: true },
+            X_A_init: { value: 0.001, required: true },
+            X_TS_init: { value: 125.0009, required: true },
+
+            timeStep: { value: 1, required: true },
+
+            enableLog: { value: false },
+            logLevel: { value: "error" },
+
+            positionVsParent: { value: "" }
+        },
+        inputs: 1,
+        outputs: 3,
+        inputLabels: ["input"],
+        outputLabels: ["process", "dbase", "parent"],
+        icon: "font-awesome/fa-recycle",
+        label: function() {
+            return this.name || "Reactor";
+        },
+        oneditprepare: function() {
+            // wait for the menu scripts to load
+            const waitForMenuData = () => {
+                if (window.EVOLV?.nodes?.reactor?.initEditor) {
+                    window.EVOLV.nodes.reactor.initEditor(this);
+                } else {
+                    setTimeout(waitForMenuData, 50);
+                }
+            };
+            waitForMenuData();
+
+            $("#node-input-volume").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-length").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-resolution_L").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-kla").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $(".concentrations").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-reactor_type").typedInput({
+                types: [
+                    {
+                        value: "CSTR",
+                        options: [
+                            { value: "CSTR", label: "CSTR"},
+                            { value: "PFR", label: "PFR"}
+                        ]
+                    }
+                ]
+            })
+            $("#node-input-reactor_type").on("change", function() {
+                const type = $("#node-input-reactor_type").typedInput("value");
+                if (type === "CSTR") {
+                    $(".PFR").hide();
+                } else {
+                    $(".PFR").show();
+                }
+            });
+            $("#node-input-timeStep").typedInput({
+                type:"num",
+                types:["num"]
+            })
+            // Set initial visibility on dialog open
+            const initialType = $("#node-input-reactor_type").typedInput("value");
+            if (initialType === "CSTR") {
+                $(".PFR").hide();
+            } else {
+                $(".PFR").show();
+            }
+
+            const updateDx = () => {
+                const length = parseFloat($("#node-input-length").val()) || 0;
+                const resolution = parseFloat($("#node-input-resolution_L").val()) || 1;
+                const dx = resolution > 0 ? (length / resolution).toFixed(6) : "N/A";
+                $("#dx-output").text(dx + " m");
+            };
+
+            // Set up event listeners for real-time updates
+            $("#node-input-length, #node-input-resolution_L").on("change keyup", updateDx);
+            
+            // Initial calculation
+            updateDx();
+        },
+        oneditsave: function() {
+            // save logger fields
+            if (window.EVOLV?.nodes?.reactor?.loggerMenu?.saveEditor) {
+                window.EVOLV.nodes.reactor.loggerMenu.saveEditor(this);
+            }
+
+            // save position field
+            if (window.EVOLV?.nodes?.measurement?.positionMenu?.saveEditor) {
+                window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
+            }
+
+            let volume = parseFloat($("#node-input-volume").typedInput("value"));
+            if (isNaN(volume) || volume <= 0) {
+                RED.notify("Fluid volume not set correctly", {type: "error"});
+            }
+        }
+    });
+</script>
+
+<script type="text/html" data-template-name="reactor">
+    <div class="form-row">
+        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
+        <input type="text" id="node-input-name" placeholder="Name">
+    </div>
+    <h2> Reactor properties </h2>
+    <div class="form-row">
+        <label for="node-input-reactor_type"><i class="fa fa-tag"></i> Reactor type</label>
+        <input type="text" id="node-input-reactor_type">
+    </div>
+    <div class="form-row">
+        <label for="node-input-volume"><i class="fa fa-tag"></i> Fluid volume [m3]</label>
+        <input type="text" id="node-input-volume" placeholder="m3">
+    </div>
+    <div class="form-row PFR">
+        <label for="node-input-length"><i class="fa fa-tag"></i> Reactor length [m]</label>
+        <input type="text" id="node-input-length" placeholder="m">
+    </div>
+    <h2> Simulation parameters </h2>
+    <div class="form-row">
+        <label for="node-input-timeStep"><i class="fa fa-tag"></i> Time step [s]</label>
+        <input type="text" id="node-input-timeStep" placeholder="s">
+    </div>
+    <div class="form-row PFR">
+        <label for="node-input-resolution_L"><i class="fa fa-tag"></i> Spatial resolution</label>
+        <input type="text" id="node-input-resolution_L" placeholder="#">
+    </div>
+    <div class="form-row PFR">
+        <label for="node-input-dx"><i class="fa fa-tag"></i> Δx (length / resolution) [m]</label>
+        <span id="dx-output" style="display: inline-block; padding: 8px; font-weight: bold;">--</span>
+    </div>
+    <h3> Internal mass transfer calculation (optional) </h3>
+    <div class="form-row">
+        <label for="node-input-kla"><i class="fa fa-tag"></i> kLa [d-1]</label>
+        <input type="text" id="node-input-kla" placeholder="d-1">
+    </div>
+    <h2> Dissolved components </h2>
+    <div class="form-row">
+        <label for="node-input-S_O_init"><i class="fa fa-tag"></i> Initial dissolved oxygen [g O2 m-3]</label>
+        <input type="text" id="node-input-S_O_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_I_init"><i class="fa fa-tag"></i> Initial soluble inert  organics [g COD m-3]</label>
+        <input type="text" id="node-input-S_I_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_S_init"><i class="fa fa-tag"></i> Initial readily biodegrable substrates [g COD m-3]</label>
+        <input type="text" id="node-input-S_S_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_NH_init"><i class="fa fa-tag"></i> Initial ammonium / ammonia [g N m-3]</label>
+        <input type="text" id="node-input-S_NH_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_N2_init"><i class="fa fa-tag"></i> Initial dinitrogen, released by denitrification [g N m-3]</label>
+        <input type="text" id="node-input-S_N2_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_NO_init"><i class="fa fa-tag"></i> Initial nitrite + nitrate [g N m-3]</label>
+        <input type="text" id="node-input-S_NO_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-S_HCO_init"><i class="fa fa-tag"></i> Initial alkalinity, bicarbonate [mole HCO3- m-3]</label>
+        <input type="text" id="node-input-S_HCO_init" class="concentrations">
+    </div>
+    <h2> Particulate components </h2>
+    <div class="form-row">
+        <label for="node-input-X_I_init"><i class="fa fa-tag"></i> Initial inert particulate organics [g COD m-3]</label>
+        <input type="text" id="node-input-X_I_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-X_S_init"><i class="fa fa-tag"></i> Initial slowly biodegrable substrates [g COD m-3]</label>
+        <input type="text" id="node-input-X_S_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-X_H_init"><i class="fa fa-tag"></i> Initial heterotrophic biomass [g COD m-3]</label>
+        <input type="text" id="node-input-X_H_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-X_STO_init"><i class="fa fa-tag"></i> Initial Organics stored by heterotrophs [g COD m-3]</label>
+        <input type="text" id="node-input-X_STO_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-X_A_init"><i class="fa fa-tag"></i> Initial autotrophic, nitrifying biomass [g COD m-3]</label>
+        <input type="text" id="node-input-X_A_init" class="concentrations">
+    </div>
+    <div class="form-row">
+        <label for="node-input-X_TS_init"><i class="fa fa-tag"></i> Initial total suspended solids [g TSS m-3]</label>
+        <input type="text" id="node-input-X_TS_init" class="concentrations">
+    </div>
+
+    <!-- Logger fields injected here -->
+	<div id="logger-fields-placeholder"></div>
+
+    <!-- Position fields will be injected here -->
+    <div id="position-fields-placeholder"></div>
+
+</script>
+
+<script type="text/html" data-help-name="reactor">
+    <p>New reactor node</p>
+</script>
--- a/reactor.js
+++ b/reactor.js
@@ -0,0 +1,26 @@
+const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
+const nodeClass = require('./src/nodeClass.js'); // node class
+const { MenuManager } = require('generalFunctions');
+
+
+module.exports = function (RED) {
+    // Register the node type
+    RED.nodes.registerType(nameOfNode, function (config) {
+        // Initialize the Node-RED node first
+        RED.nodes.createNode(this, config);
+        // Then create your custom class and attach it
+        this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
+    });
+
+    const menuMgr = new MenuManager();
+
+    // Serve /advancedReactor/menu.js
+    RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
+        try {
+            const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
+            res.type('application/javascript').send(script);
+        } catch (err) {
+            res.status(500).send(`// Error generating menu: ${err.message}`);
+        }
+    });
+};
--- a/src/nodeClass.js
+++ b/src/nodeClass.js
@@ -0,0 +1,159 @@
+const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
+
+
+class nodeClass {
+    /**
+    * Node-RED node class for advanced-reactor.
+    * @param {object} uiConfig - Node-RED node configuration
+    * @param {object} RED - Node-RED runtime API
+    * @param {object} nodeInstance - Node-RED node instance
+    * @param {string} nameOfNode - Name of the node
+    */
+    constructor(uiConfig, RED, nodeInstance, nameOfNode) {
+        // Preserve RED reference for HTTP endpoints if needed
+        this.node = nodeInstance;
+        this.RED = RED;
+        this.name = nameOfNode;
+        this.source = null;
+
+        this._loadConfig(uiConfig)
+        this._setupClass();
+
+        this._attachInputHandler();
+        this._registerChild();
+        this._startTickLoop();
+        this._attachCloseHandler();
+    }
+
+    /**
+     * Handle node-red input messages
+     */
+    _attachInputHandler() {
+        this.node.on('input', (msg, send, done) => {
+
+            switch (msg.topic) {
+                case "clock":
+                    this.source.updateState(msg.timestamp);
+                    break;
+                case "Fluent":
+                    this.source.setInfluent = msg;
+                    break;
+                case "OTR":
+                    this.source.setOTR = msg;
+                    break;
+                case "Dispersion":
+                    this.source.setDispersion = msg;
+                    break;
+                case 'registerChild':
+                    // Register this node as a parent of the child node
+                    const childId = msg.payload;
+                    const childObj = this.RED.nodes.getNode(childId); 
+                    this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
+                    break;
+                default:
+                    console.log("Unknown topic: " + msg.topic);
+            }
+
+            if (done) {
+                done();
+            }
+        });
+    }
+
+    /**
+     * Parse node configuration
+     * @param {object} uiConfig Config set in UI in node-red
+     */
+    _loadConfig(uiConfig) {
+        this.config = {
+            general: {
+                name: uiConfig.name || this.name,
+                id: this.node.id,
+                unit: null,
+                logging: {
+                    enabled: uiConfig.enableLog,
+                    logLevel: uiConfig.logLevel
+                }
+            },
+            functionality: {
+                positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
+                softwareType: "reactor" // should be set in config manager
+            },
+            reactor_type: uiConfig.reactor_type,
+            volume: parseFloat(uiConfig.volume),
+            length: parseFloat(uiConfig.length),
+            resolution_L: parseInt(uiConfig.resolution_L),
+            kla: parseFloat(uiConfig.kla),
+            initialState: [
+                parseFloat(uiConfig.S_O_init),
+                parseFloat(uiConfig.S_I_init),
+                parseFloat(uiConfig.S_S_init),
+                parseFloat(uiConfig.S_NH_init),
+                parseFloat(uiConfig.S_N2_init),
+                parseFloat(uiConfig.S_NO_init),
+                parseFloat(uiConfig.S_HCO_init),
+                parseFloat(uiConfig.X_I_init),
+                parseFloat(uiConfig.X_S_init),
+                parseFloat(uiConfig.X_H_init),
+                parseFloat(uiConfig.X_STO_init),
+                parseFloat(uiConfig.X_A_init),
+                parseFloat(uiConfig.X_TS_init)
+            ],
+            timeStep: parseFloat(uiConfig.timeStep)
+        }
+    }
+
+    /**
+     * Register this node as a child upstream and downstream.
+     * Delayed to avoid Node-RED startup race conditions.
+     */
+    _registerChild() {
+        setTimeout(() => {
+        this.node.send([
+            null,
+            null,
+            { topic: 'registerChild', payload: this.node.id, positionVsParent: this.config?.functionality?.positionVsParent || 'atEquipment' }
+        ]);
+        }, 100);
+    }
+
+    /**
+     * Setup reactor class based on config
+     */
+    _setupClass() {
+        let new_reactor;
+
+        switch (this.config.reactor_type) {
+            case "CSTR":
+                new_reactor = new Reactor_CSTR(this.config);
+                break;
+            case "PFR":
+                new_reactor = new Reactor_PFR(this.config);
+                break;
+            default:
+                console.warn("Unknown reactor type: " + uiConfig.reactor_type);
+        }
+
+        this.source = new_reactor; // protect from reassignment
+        this.node.source = this.source;
+    }
+
+    _startTickLoop() {
+        setTimeout(() => {
+            this._tickInterval = setInterval(() => this._tick(), 1000);
+        }, 1000);
+    }
+
+    _tick(){
+        this.node.send([this.source.getEffluent, null, null]);
+    }
+
+    _attachCloseHandler() {
+        this.node.on('close', (done) => {
+            clearInterval(this._tickInterval);
+            done();
+        });
+    }
+}
+
+module.exports = nodeClass;
--- a/src/reaction_modules/asm3_class
+++ b/src/reaction_modules/asm3_class
@@ -0,0 +1,222 @@
+const math = require('mathjs');
+
+const ASM_CONSTANTS = {
+  S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
+  NUM_SPECIES: 13
+};
+
+const KINETIC_CONSTANTS = {
+  // Hydrolysis
+  k_H:      9.,   // 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:    12.,  // storage rate constant          [g S_S g-1 X_H d-1]
+  nu_NO:    0.5,  // 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:      10.,  // saturation constant S_s        [g COD m-3]
+  K_STO:    0.1,  // saturation constant X_STO      [g X_STO g-1 X_H]
+  mu_H_max: 3.,   // 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:    0.3,  // aerobic respiration rate       [d-1]
+  b_H_NO:   0.15, // anoxic respiration rate        [d-1]
+  b_STO_O:  0.3,  // aerobic respitation rate X_STO [d-1]
+  b_STO_NO: 0.15, // anoxic respitation rate X_STO  [d-1]
+  // Autotrophs
+  mu_A_max: 1.3,  // maximum specific growth rate   [d-1]
+  K_A_NH:   1.4,  // 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:    0.20, // aerobic respiration rate       [d-1]
+  b_A_NO:   0.10  // anoxic respiration rate        [d-1]
+};
+
+const STOICHIOMETRIC_CONSTANTS = {
+  // Fractions
+  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:  0.80, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
+  Y_STO_NO: 0.70, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
+  Y_H_O:    0.80, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
+  Y_H_NO:   0.65, // 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:    0.04, // nitrogen content X_I           [g N g-1 X_I]
+  i_NXS:    0.03, // 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]
+};
+
+/**
+ * ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters.
+ */
+class ASM3 {
+
+  constructor() {
+    /**
+     * Kinetic parameters for ASM3 at 20 C. Using Koch et al. 2000 parameters.
+     * @property {Object} kin_params - Kinetic parameters
+     */
+    this.kin_params = KINETIC_CONSTANTS;
+
+    /**
+     * Stoichiometric and composition parameters for ASM3. Using Koch et al. 2000 parameters.
+     * @property {Object} stoi_params - Stoichiometric parameters
+     */
+    this.stoi_params = STOICHIOMETRIC_CONSTANTS;
+
+    /**
+     * Temperature theta parameters for ASM3. Using Koch et al. 2000 parameters.
+     * These parameters are used to adjust reaction rates based on temperature.
+     * @property {Object} temp_params - Temperature theta parameters
+     */
+    this.temp_params = {
+      // Hydrolysis
+      theta_H:        0.04,
+      // Heterotrophs
+      theta_STO:      0.07,
+      theta_mu_H:     0.07,
+      theta_b_H_O:    0.07,
+      theta_b_H_NO:   0.07,
+      theta_b_STO_O:  this._compute_theta(0.1, 0.3, 10, 20),
+      theta_b_STO_NO: this._compute_theta(0.05, 0.15, 10, 20),
+      // Autotrophs
+      theta_mu_A:     0.105,
+      theta_b_A_O:    0.105,
+      theta_b_A_NO:   0.105
+    };
+
+    this.stoi_matrix = this._initialise_stoi_matrix();
+  }
+
+  /**
+   * Initialises the stoichiometric matrix for ASM3.
+   * @returns {Array} - The stoichiometric matrix for ASM3. (2D array)
+   */
+  _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
+  }
+
+  /**
+   * Computes the Monod equation rate value for a given concentration and half-saturation constant.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species.
+   * @returns {number} - Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _monod(c, K) {
+    return c / (K + c);
+  }
+
+  /**
+   * Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species. 
+   * @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _inv_monod(c, K) {
+    return K / (K + c);
+  }
+
+  /**
+   * Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter.
+   * @param {number} k - Rate constant at 20 degrees Celcius.
+   * @param {number} theta - Theta parameter.
+   * @param {number} T - Temperature in Celcius.
+   * @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation.
+   */
+  _arrhenius(k, theta, T) {
+    return k * Math.exp(theta*(T-20));
+  }
+
+  /**
+   * Computes the temperature theta parameter based on two rate constants and their corresponding temperatures.
+   * @param {number} k1 - Rate constant at temperature T1.
+   * @param {number} k2 - Rate constant at temperature T2.
+   * @param {number} T1 - Temperature T1 in Celcius.
+   * @param {number} T2 - Temperature T2 in Celcius.
+   * @returns {number} - Theta parameter.
+   */
+  _compute_theta(k1, k2, T1, T2) {
+    return Math.log(k1/k2)/(T1-T2);
+  }
+
+  /**
+   * Computes the reaction rates for each process reaction based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Reaction rates for each process reaction.
+   */
+  compute_rates(state, T = 20) {
+    // 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;
+    const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
+
+    // Hydrolysis
+    rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H;
+
+    // Heterotrophs
+    rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H;
+    rates[2] = this._arrhenius(k_STO, theta_STO, T) * 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] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * 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] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * 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] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H;
+    rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO;
+    
+    // Autotrophs
+    rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * 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] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A;
+    rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A;
+    
+    return rates;
+  }
+
+  /**
+   * Computes the change in concentrations of reaction species based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Change in reaction species concentrations.
+   */
+  compute_dC(state, T = 20) { // 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, T));
+  }
+}
+
+module.exports = { ASM3, ASM_CONSTANTS, KINETIC_CONSTANTS, STOICHIOMETRIC_CONSTANTS };
--- a/src/reaction_modules/asm3_class.js
+++ b/src/reaction_modules/asm3_class.js
@@ -0,0 +1,222 @@
+const math = require('mathjs');
+
+const ASM_CONSTANTS = {
+  S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
+  NUM_SPECIES: 13
+};
+
+const KINETIC_CONSTANTS = {
+  // 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]
+};
+
+const STOICHIOMETRIC_CONSTANTS = {
+  // Fractions
+  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]
+};
+
+/**
+ * ASM3 class for the Activated Sludge Model No. 3 (ASM3).
+ */
+class ASM3 {
+
+  constructor() {
+    /**
+     * Kinetic parameters for ASM3 at 20 C.
+     * @property {Object} kin_params - Kinetic parameters
+     */
+    this.kin_params = KINETIC_CONSTANTS;
+
+    /**
+     * Stoichiometric and composition parameters for ASM3.
+     * @property {Object} stoi_params - Stoichiometric parameters
+     */
+    this.stoi_params = STOICHIOMETRIC_CONSTANTS;
+
+    /**
+     * Temperature theta parameters for ASM3.
+     * These parameters are used to adjust reaction rates based on temperature.
+     * @property {Object} temp_params - Temperature theta parameters
+     */
+    this.temp_params = {
+      // Hydrolysis
+      theta_H:        this._compute_theta(2, 3, 10, 20),
+      // Heterotrophs
+      theta_STO:      this._compute_theta(2.5, 5, 10, 20),
+      theta_mu_H:     this._compute_theta(1, 2, 10, 20),
+      theta_b_H_O:    this._compute_theta(0.1, 0.2, 10, 20),
+      theta_b_H_NO:   this._compute_theta(0.05, 0.1, 10, 20),
+      theta_b_STO_O:  this._compute_theta(0.1, 0.2, 10, 20),
+      theta_b_STO_NO: this._compute_theta(0.05, 0.1, 10, 20),
+      // Autotrophs
+      theta_mu_A:     this._compute_theta(0.35, 1, 10, 20),
+      theta_b_A_O:    this._compute_theta(0.05, 0.15, 10, 20),
+      theta_b_A_NO:   this._compute_theta(0.02, 0.05, 10, 20)
+    };
+
+    this.stoi_matrix = this._initialise_stoi_matrix();
+  }
+
+  /**
+   * Initialises the stoichiometric matrix for ASM3.
+   * @returns {Array} - The stoichiometric matrix for ASM3. (2D array)
+   */
+  _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
+  }
+
+  /**
+   * Computes the Monod equation rate value for a given concentration and half-saturation constant.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species.
+   * @returns {number} - Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _monod(c, K) {
+    return c / (K + c);
+  }
+
+  /**
+   * Computes the inverse Monod equation rate value for a given concentration and half-saturation constant. Used for inhibition.
+   * @param {number} c - Concentration of reaction species.
+   * @param {number} K - Half-saturation constant for the reaction species. 
+   * @returns {number} - Inverse Monod equation rate value for the given concentration and half-saturation constant.
+   */
+  _inv_monod(c, K) {
+    return K / (K + c);
+  }
+
+  /**
+   * Adjust the rate parameter for temperature T using simplied Arrhenius equation based on rate constant at 20 degrees Celsius and theta parameter.
+   * @param {number} k - Rate constant at 20 degrees Celcius.
+   * @param {number} theta - Theta parameter.
+   * @param {number} T - Temperature in Celcius.
+   * @returns {number} - Adjusted rate parameter at temperature T based on the Arrhenius equation.
+   */
+  _arrhenius(k, theta, T) {
+    return k * Math.exp(theta*(T-20));
+  }
+
+  /**
+   * Computes the temperature theta parameter based on two rate constants and their corresponding temperatures.
+   * @param {number} k1 - Rate constant at temperature T1.
+   * @param {number} k2 - Rate constant at temperature T2.
+   * @param {number} T1 - Temperature T1 in Celcius.
+   * @param {number} T2 - Temperature T2 in Celcius.
+   * @returns {number} - Theta parameter.
+   */
+  _compute_theta(k1, k2, T1, T2) {
+    return Math.log(k1/k2)/(T1-T2);
+  }
+
+  /**
+   * Computes the reaction rates for each process reaction based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Reaction rates for each process reaction.
+   */
+  compute_rates(state, T = 20) {
+    // 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;
+    const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
+
+    // Hydrolysis
+    rates[0] = X_H == 0 ? 0 : this._arrhenius(k_H, theta_H, T) * this._monod(X_S / X_H, K_X) * X_H;
+
+    // Heterotrophs
+    rates[1] = this._arrhenius(k_STO, theta_STO, T) * this._monod(S_O, K_O) * this._monod(S_S, K_S) * X_H;
+    rates[2] = this._arrhenius(k_STO, theta_STO, T) * 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] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * 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] = X_H == 0 ? 0 : this._arrhenius(mu_H_max, theta_mu_H, T) * 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] = this._arrhenius(b_H_O, theta_b_H_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[6] = this._arrhenius(b_H_NO, theta_b_H_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_H;
+    rates[7] = this._arrhenius(b_STO_O, theta_b_STO_O, T) * this._monod(S_O, K_O) * X_H;
+    rates[8] = this._arrhenius(b_STO_NO, theta_b_STO_NO, T) * this._inv_monod(S_O, K_O) * this._monod(S_NO, K_NO) * X_STO;
+    
+    // Autotrophs
+    rates[9] = this._arrhenius(mu_A_max, theta_mu_A, T) * 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] = this._arrhenius(b_A_O, theta_b_A_O, T) * this._monod(S_O, K_O) * X_A;
+    rates[11] = this._arrhenius(b_A_NO, theta_b_A_NO, T) * this._inv_monod(S_O, K_A_O) * this._monod(S_NO, K_NO) * X_A;
+    
+    return rates;
+  }
+
+  /**
+   * Computes the change in concentrations of reaction species based on the current state and temperature.
+   * @param {Array} state - State vector containing concentrations of reaction species.
+   * @param {number} [T=20] - Temperature in degrees Celsius (default is 20).
+   * @returns {Array} - Change in reaction species concentrations.
+   */
+  compute_dC(state, T = 20) { // 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, T));
+  }
+}
+
+module.exports = { ASM3, ASM_CONSTANTS, KINETIC_CONSTANTS, STOICHIOMETRIC_CONSTANTS };
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -0,0 +1,488 @@
+const { ASM3, ASM_CONSTANTS } = require('./reaction_modules/asm3_class.js');
+const { create, all, isArray } = require('mathjs');
+const { assertNoNaN } = require('./utils.js');
+const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
+const EventEmitter = require('events');
+
+const mathConfig = {
+  matrix: 'Array' // use Array as the matrix type
+};
+
+const math = create(all, mathConfig);
+
+const BC_PADDING = 2; // Boundary Condition padding for open boundaries in extendedState variable
+const DEBUG = false;
+const DAY2MS = 1000 * 60 * 60 * 24; // convert between days and milliseconds
+
+class Reactor {
+  /**
+   * Reactor base class.
+   * @param {object} config - Configuration object containing reactor parameters.
+   */
+  constructor(config) {
+    this.config = config;
+    // EVOLV stuff
+    this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name);
+    this.emitter = new EventEmitter();
+    this.measurements = new MeasurementContainer();
+    this.childRegistrationUtils = new childRegistrationUtils(this); // child registration utility
+
+    // placeholder variables for children and parents
+    this.upstreamReactor = null;
+    this.downstreamReactor = null;
+    this.returnPump = null;
+
+    this.asm = new ASM3(); // Reaction model
+
+    this.volume = config.volume; // fluid volume reactor [m3]
+
+    this.Fs = [0]; // fluid debits per inlet [m3 d-1]
+    this.Cs_in = [Array(ASM_CONSTANTS.NUM_SPECIES).fill(0)]; // composition influents
+    this.OTR = 0.0; // oxygen transfer rate [g O2 d-1 m-3]
+    this.temperature = 20; // temperature [C]
+
+    this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
+
+    this.currentTime = null; // milliseconds since epoch [ms]
+    this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
+    this.speedUpFactor = 1; // 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) {
+    const i_in = input.payload.inlet;
+    if (this.Fs.length <= i_in) {
+      this.logger.debug(`Adding new inlet index ${i_in}.`);
+      this.Fs.push(0);
+      this.Cs_in.push(Array(ASM_CONSTANTS.NUM_SPECIES).fill(0));
+      this.setInfluent = input;
+    }
+    this.Fs[i_in] = input.payload.F;
+    this.Cs_in[i_in] = input.payload.C;
+  }
+
+  /**
+   * Setter for OTR (Oxygen Transfer Rate).
+   * @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1 m-3].
+   */
+  set setOTR(input) {
+    this.OTR = input.payload;
+  }
+
+  /**
+   * Getter for effluent data.
+   * @returns {object} Effluent data object (msg).
+   */
+  get getEffluent() {
+    const Cs = isArray(this.state.at(-1)) ? this.state.at(-1) : this.state;
+    const effluent = [{ topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: Cs }, timestamp: this.currentTime }];
+    if (this.returnPump) {
+      const recirculationFlow = this.returnPump.measurements.type("flow").variant("measured").position("atEquipment").getCurrentValue();
+      // constrain flow to prevent negatives
+      const F_main = Math.max(effluent[0].payload.F - recirculationFlow, 0);
+      const F_sidestream = effluent[0].payload.F < recirculationFlow ? effluent[0].payload.F : recirculationFlow;
+      effluent[0].payload.F = F_main;
+      effluent.push({ topic: "Fluent", payload: { inlet: 1, F: F_sidestream, C: Cs }, timestamp: this.currentTime });
+    }
+    return effluent;
+  }
+
+  /**
+   * Calculate the oxygen transfer rate (OTR) based on the dissolved oxygen concentration and temperature.
+   * @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
+   * @param {number} T - Temperature in Celsius, default to 20 C.
+   * @returns {number} - Calculated OTR [g O2 d-1 m-3].
+   */
+  _calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C
+    const 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;
+    }
+  }
+
+  /**
+   * Register child function required for child registration.
+   * @param {object} child 
+   * @param {string} softwareType 
+   */
+  registerChild(child, softwareType) {
+    if(!child) {
+      this.logger.error(`Invalid ${softwareType} child provided.`);
+      return;
+    }
+
+    switch (softwareType) {
+      case "measurement":
+        this.logger.debug(`Registering measurement child...`);
+        this._connectMeasurement(child);
+        break;
+      case "reactor":
+        this.logger.debug(`Registering reactor child...`);
+        this._connectReactor(child);
+        break;
+      case "machine":
+        this.logger.debug(`Registering machine child...`);
+        this._connectMachine(child);
+        break;
+
+      default:
+        this.logger.error(`Unrecognized softwareType: ${softwareType}`);
+    }
+  }
+
+  _connectMeasurement(measurementChild) {
+    const position = measurementChild.config.functionality.positionVsParent;
+    const measurementType = measurementChild.config.asset.type;
+    const eventName = `${measurementType}.measured.${position}`;
+
+    // Register event listener for measurement updates
+    measurementChild.measurements.emitter.on(eventName, (eventData) => {
+      this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
+
+      // Store directly in parent's measurement container
+      this.measurements
+        .type(measurementType)
+        .variant("measured")
+        .position(position)
+        .value(eventData.value, eventData.timestamp, eventData.unit);
+      
+      this._updateMeasurement(measurementType, eventData.value, position, eventData);
+    });
+  }
+
+
+  _connectReactor(reactorChild) {
+    if (reactorChild.config.functionality.positionVsParent != "upstream") {
+      this.logger.warn("Reactor children of other reactors should always be upstream!");
+    }
+
+    // set upstream and downstream reactor variable in current and child nodes respectively for easy access
+    this.upstreamReactor = reactorChild;
+    reactorChild.downstreamReactor = this;
+
+    reactorChild.emitter.on("stateChange", (eventData) => { // Triggers state update in downstream reactor.
+      this.logger.debug(`State change of upstream reactor detected.`);
+      this.updateState(eventData);
+    });
+  }
+
+  _connectMachine(machineChild) {
+    if (machineChild.config.functionality.positionVsParent == "downstream") {
+      machineChild.upstreamSource = this;
+      this.returnPump = machineChild;
+    }
+  }
+  
+  _updateMeasurement(measurementType, value, position, context) {
+    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
+    switch (measurementType) {
+      case "temperature":
+        if (position == "atEquipment") {
+          this.temperature = value;
+        }
+        break;
+      default:
+        this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
+        return;
+    }
+  }
+
+  /**
+   * 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) {
+    if (!this.currentTime) { // initialise currentTime variable
+      this.currentTime = newTime;
+      return;
+    }
+
+    if (this.upstreamReactor) { // grab main effluent upstream reactor
+      this.setInfluent = this.upstreamReactor.getEffluent[0];
+    }
+
+    const n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
+
+    if (n_iter == 0) { // no update required, change in currentTime smaller than time step
+      return;
+    }
+
+    let n = 0;
+    while (n < n_iter) {
+      this.tick(this.timeStep);
+      n += 1;
+    }
+    this.currentTime += n_iter * this.timeStep * DAY2MS / this.speedUpFactor;
+    this.emitter.emit("stateChange", this.currentTime); // update downstream reactors
+
+    if (this.returnPump) { // update recirculation pump state
+      this.returnPump.updateSourceSink();
+    }
+  }
+}
+
+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;
+  }
+
+  _updateMeasurement(measurementType, value, position, context) {
+
+    switch(measurementType) {
+      case "quantity (oxygen)":
+        this.state[ASM_CONSTANTS.S_O_INDEX] = value;
+        break;
+      case "quantity (ammonium)":
+        this.state[ASM_CONSTANTS.S_NH_INDEX] = value;
+        break;
+      case "quantity (nox)":
+        this.state[ASM_CONSTANTS.S_NO_INDEX] = value;
+        break;
+      default:
+        super._updateMeasurement(measurementType, value, position, context);
+    }
+  }
+
+  /**
+   * 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, this.temperature);
+    const transfer = Array(ASM_CONSTANTS.NUM_SPECIES).fill(0.0);
+    transfer[ASM_CONSTANTS.S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[ASM_CONSTANTS.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
+    if(DEBUG){
+      assertNoNaN(dC_total, "change in state");
+      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());
+    this.extendedState = Array.from(Array(this.n_x + 2*BC_PADDING), () => new Array(ASM_CONSTANTS.NUM_SPECIES).fill(0));
+
+    // initialise extended state
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+
+    this.D = 0.0; // axial dispersion [m2 d-1]
+
+    this.D_op = this._makeDoperator();
+    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 = this._constrainDispersion(input.payload);
+  }
+
+  _connectReactor(reactorChild) {
+    if (math.abs(reactorChild.d_x - this.d_x) / this.d_x < 0.025) {
+      this.logger.warn("Significant grid sizing discrepancies between adjacent reactors! Change resolutions to match reactors grid step, or implement boundary value interpolation.");
+    }
+    super._connectReactor(reactorChild);
+  }
+
+  /**
+   * Update the reactor state based on the new time. Performs checks specific to PFR.
+   * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
+   */
+  updateState(newTime) {
+    super.updateState(newTime);
+    
+    this.D = this._constrainDispersion(this.D); // constrains D to minimum dispersion, so that local Péclet number is always above 2
+    const Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
+
+    (Co_D >= 0.5) && this.logger.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);
+    }
+  }
+
+  /**
+   * 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) {
+    this._applyBoundaryConditions();
+
+    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
+    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.extendedState);
+    const reaction = this.extendedState.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
+    const transfer = Array.from(Array(this.n_x+2*BC_PADDING), () => new Array(ASM_CONSTANTS.NUM_SPECIES).fill(0));
+
+    if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
+      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
+      }
+    } else {
+      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature);
+      }
+    }
+
+    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
+
+    const stateNew = math.add(this.state, dC_total);
+
+    if (DEBUG) {
+      assertNoNaN(dispersion, "dispersion");
+      assertNoNaN(advection, "advection");
+      assertNoNaN(reaction, "reaction");
+      assertNoNaN(dC_total, "change in state");
+      assertNoNaN(stateNew, "new state post BC");
+    }
+
+    this.state = this._arrayClip2Zero(stateNew);
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+    return stateNew;
+  }
+
+  _updateMeasurement(measurementType, value, position, context) {
+    const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+
+    // naive approach for reconciling measurements and simulation
+    // could benefit from Kalman filter?
+    switch(measurementType) {
+      case "quantity (oxygen)":
+        this.state[grid_pos][ASM_CONSTANTS.S_O_INDEX] = value;
+        break;
+      case "quantity (ammonium)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NH_INDEX] = value;
+        break;
+      case "quantity (nox)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NO_INDEX] = value;
+        break;
+      default:
+        super._updateMeasurement(measurementType, value, position, context);
+    }
+  }
+
+  /**
+   * 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)
+   */
+  _applyBoundaryConditions() {
+    // Upstream BC
+    if (this.upstreamReactor && this.upstreamReactor.config.reactor_type == "PFR") {
+      // Open boundary, if upstream reactor is PFR
+      this.extendedState.splice(0, BC_PADDING, ...this.upstreamReactor.state.slice(-BC_PADDING)); 
+    } else {
+      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 = this.D*this.A/(math.sum(this.Fs)*this.d_x);
+        this.extendedState[BC_PADDING] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, this.extendedState[BC_PADDING+1])));
+        // Numerical boundary condition (first-order accurate)
+        this.extendedState[BC_PADDING-1] = math.add(math.multiply(2, this.extendedState[BC_PADDING]), math.multiply(-2, this.extendedState[BC_PADDING+2]), this.extendedState[BC_PADDING+3]);
+      } else {
+        // Neumann BC (no flux)
+        this.extendedState.fill(this.extendedState[BC_PADDING], 0, BC_PADDING);
+      }
+    }
+
+    // Downstream BC
+    if (this.downstreamReactor && this.downstreamReactor.config.reactor_type == "PFR") {
+      // Open boundary, if downstream reactor is PFR
+      this.extendedState.splice(this.n_x+BC_PADDING, BC_PADDING, ...this.downstreamReactor.state.slice(0, BC_PADDING));
+    } else {
+      // Neumann BC (no flux)
+      this.extendedState.fill(this.extendedState.at(-1-BC_PADDING), BC_PADDING+this.n_x);
+    }
+  }
+
+  /**
+   * Create finite difference first derivative operator.
+   */
+  _makeDoperator() { // create gradient operator
+    const D_size = this.n_x+2*BC_PADDING;
+    const I = math.resize(math.diag(Array(D_size).fill(1/12), -2), [D_size, D_size]);
+    const A = math.resize(math.diag(Array(D_size).fill(-2/3), -1), [D_size, D_size]);
+    const B = math.resize(math.diag(Array(D_size).fill(2/3), 1), [D_size, D_size]);
+    const C = math.resize(math.diag(Array(D_size).fill(-1/12), 2), [D_size, D_size]);
+    const D = math.add(I, A, B, C);
+    // set by BCs elsewhere
+    D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
+    return D;
+  }
+
+  /**
+   * Create central finite difference second derivative operator.
+   */
+  _makeD2operator() { // create the central second derivative operator
+    const D_size = this.n_x+2*BC_PADDING;
+    const I = math.diag(Array(D_size).fill(-2), 0);
+    const A = math.resize(math.diag(Array(D_size).fill(1), 1), [D_size, D_size]);
+    const B = math.resize(math.diag(Array(D_size).fill(1), -1), [D_size, D_size]);
+    const D2 = math.add(I, A, B);
+    // set by BCs elsewhere
+    D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
+    return D2;
+  }
+
+  /**
+   * Constrains dispersion so that local Péclet number stays below 2. Needed for stable central differencing method.
+   */
+  _constrainDispersion(D) {
+    const Dmin = math.sum(this.Fs) * this.d_x / (1.999 * this.A);
+    if (D < Dmin) {
+      this.logger.warn(`Local Péclet number too high! Constraining given dispersion (${D}) to minimal value (${Dmin}).`);
+      return Dmin;
+    }
+    return D;
+  }
+}
+
+module.exports = { Reactor_CSTR, Reactor_PFR };
--- a/src/utils.js
+++ b/src/utils.js
@@ -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 };
Author	SHA1	Message	Date
p.vanderwilt	7eecbddd19	Add example flow	2025-11-28 14:29:53 +01:00
p.vanderwilt	d56e422d90	Shift fields around in node parameters	2025-11-28 11:52:40 +01:00
p.vanderwilt	61f911af6b	Update README.md	2025-11-28 10:51:10 +00:00
p.vanderwilt	9c3a32c2cb	Merge pull request 'Final bug fixes and documentation' (#6 ) from dev-Pieter into main Reviewed-on: #6	2025-11-21 13:48:18 +00:00
p.vanderwilt	033a56a9e0	Enhance comments and documentation in Reactor classes for clarity and maintainability	2025-11-21 12:29:46 +01:00
p.vanderwilt	dd70b8c890	Fix CSTR PFR distinctions	2025-11-21 11:02:40 +01:00
p.vanderwilt	3d93f2a7b9	Fix minor bug	2025-11-14 14:48:39 +01:00
p.vanderwilt	cc89833530	Update state handling in reactor class and optimize time iteration logic	2025-11-14 13:11:09 +01:00
p.vanderwilt	f3bbf63602	Add return pump update in reactor state change	2025-11-14 12:55:34 +01:00
p.vanderwilt	70af0885e3	Prepare for working with relative time	2025-11-14 12:34:52 +01:00
p.vanderwilt	dbfc4a81b2	Remove unused / depreciated input handling	2025-11-14 12:33:16 +01:00
p.vanderwilt	f14e2c8d8e	Reformat asm constants	2025-11-13 16:52:38 +01:00
p.vanderwilt	7e34b9aa71	Add real-time calculation for dx based on length and resolution inputs	2025-11-13 13:59:56 +01:00
p.vanderwilt	ff814074a4	Merge pull request 'Minor bug fixes, code perfomance and clarity improvements' (#5 ) from dev-Pieter into main Reviewed-on: #5	2025-11-12 09:27:38 +00:00
p.vanderwilt	2b37163a8a	Minor fixes	2025-11-07 16:51:48 +01:00
p.vanderwilt	a106276ca6	Add additional ASM constants, add other sensor handling, fix bug in kla model	2025-11-07 11:59:24 +01:00
p.vanderwilt	ffb4080f14	Refactor boundary condition handling in Reactor_PFR class for improved clarity and efficiency	2025-11-06 17:24:10 +01:00
p.vanderwilt	260d04b96f	Minor optimisations in code and clarification	2025-11-06 16:36:51 +01:00
p.vanderwilt	9f060d2dd0	Refactor, minor changes and remove depreciated functions	2025-11-06 16:09:18 +01:00
p.vanderwilt	b0dd9b6a8f	Refactor ASM3 module to export ASM_CONSTANTS and update references in Reactor classes	2025-11-06 15:47:18 +01:00
p.vanderwilt	5c41dc44a3	Clean up unused code	2025-11-06 15:46:43 +01:00
p.vanderwilt	4578667a96	Merge pull request 'Recirculation Integration' (#4 ) from recirculation-integration into main Reviewed-on: #4	2025-11-06 13:55:42 +00:00
p.vanderwilt	3828e43c12	Refactor reactor node configuration to remove n_inlets and simplify inlet handling	2025-11-06 14:51:06 +01:00
p.vanderwilt	e6923f2916	Refactor child registration and connection methods to handle invalid inputs and improve readability	2025-10-31 11:54:28 +01:00
p.vanderwilt	4680b98418	minor variable name changes	2025-10-23 17:16:10 +02:00
p.vanderwilt	eb787ec47f	Minor bug fix and change in report level when encountering invalid children	2025-10-22 14:40:56 +02:00
HorriblePerson555	6de4f9ec3e	Fix recirculation flow calculation to prevent negative flow rates and improve variable naming	2025-10-21 13:02:41 +02:00
HorriblePerson555	7b38c2f51a	Refactor recirculation flow calculation to ensure non-negative flow rates and correct measurement position	2025-10-21 12:32:21 +02:00
HorriblePerson555	018215934e	Fix recirculation flow measurement to use getCurrentValue and handle undefined values	2025-10-20 17:37:29 +02:00
HorriblePerson555	3a820df7f2	Non-functioning prototype with partial rotating machine integration	2025-10-20 16:45:53 +02:00
HorriblePerson555	670c4deacb	Merge branch 'boundary-conditions'	2025-10-16 15:36:37 +02:00
HorriblePerson555	f44bac9aab	Add warnings for reactor child positioning and grid sizing discrepancies	2025-10-16 15:30:51 +02:00
p.vanderwilt	1dc9cd0031	Add dispersion constraint	2025-10-14 12:48:43 +02:00
p.vanderwilt	2a520be33b	Refactor measurement position assignment and update grid position calculation in Reactor classes to align with new generalFunctions	2025-10-10 11:27:55 +02:00
p.vanderwilt	baecf2f599	Functioning code, requires improved sequencing	2025-10-02 17:39:31 +02:00
p.vanderwilt	cd3a19e66f	Fix boundary conditions for advection	2025-10-02 13:48:47 +02:00
p.vanderwilt	3aea0e55c4	Rewrite for improved boundary condition	2025-10-01 16:50:48 +02:00
p.vanderwilt	442ddc60ed	Fix syntax error	2025-10-01 11:50:35 +02:00
p.vanderwilt	d9511dc3c7	Implement simple BCs	2025-09-30 15:36:25 +02:00
p.vanderwilt	993482f8c0	Deal with mulitple parents and set downstreamReactor for improved boundary conditions	2025-09-29 16:58:46 +02:00
p.vanderwilt	5f4ebdc2af	Fix reference error and improve child variable naming	2025-09-29 15:45:07 +02:00
p.vanderwilt	6c79d0ef9b	Use improved boundary conditions for upstream and downstream reactors	2025-09-29 15:34:54 +02:00
p.vanderwilt	04306d0996	Fix measurement type string for oxygen in _updateMeasurement method	2025-09-29 09:40:17 +02:00
p.vanderwilt	2bc244cae7	Refactor measurement update handling in Reactor_PFR class to include default case for measurement types	2025-09-26 16:36:09 +02:00
p.vanderwilt	254f9eec5a	Fix measurement event listener to use correct measurement reference	2025-09-26 16:33:00 +02:00
p.vanderwilt	109fd182df	Refactor measurement position handling in Reactor class	2025-09-26 14:51:18 +02:00
p.vanderwilt	bf5f265a76	Update measurement handling in Reactor class and rename oxygen measurement type	2025-09-26 10:17:00 +02:00
p.vanderwilt	905674ce58	Update dependencies and correct node name	2025-09-24 15:27:08 +02:00
p.vanderwilt	da1cff55ba	Resolve merge conflicts from migration	2025-09-22 16:40:22 +02:00
p.vanderwilt	9147a3f7d0	Rename repo	2025-09-22 16:19:00 +02:00
p.vanderwilt	8f64fbe4e5	Add time step configuration and input handling in advanced reactor	2025-09-22 15:17:25 +02:00
p.vanderwilt	7a70f60655	Fix measurement event listener registration in Reactor class	2025-09-19 13:26:45 +02:00
p.vanderwilt	223c4555b8	Fix measurement reference in child registration logic	2025-09-16 15:54:31 +02:00
p.vanderwilt	972d33355e	Formatting	2025-09-16 11:44:29 +02:00
p.vanderwilt	94ea4fe76b	Fix subclass function	2025-09-15 17:39:54 +02:00
p.vanderwilt	f6b026928e	Enhance measurement child registration and update measurement handling in Reactor class	2025-09-15 12:48:18 +02:00
p.vanderwilt	c2cd29db56	Update generalFunctions dependency and enhance reactor child registration logic	2025-09-05 15:26:00 +02:00
p.vanderwilt	0b49642668	Switch general functions to new implementation	2025-09-05 13:31:42 +02:00
p.vanderwilt	a4a5266040	Update package-lock	2025-09-03 12:21:15 +02:00
p.vanderwilt	1857031027	Minor fix Koch parameters	2025-08-18 16:56:59 +02:00
p.vanderwilt	a8928e50cc	Add Koch parameters	2025-08-18 16:43:16 +02:00
p.vanderwilt	04a5b1a54f	Fix COD balance	2025-08-14 11:14:14 +02:00
p.vanderwilt	7a6825a80e	Add flows document	2025-08-04 11:45:00 +02:00
p.vanderwilt	fbbe5833b2	Temporary fix for undefined newTime value in updateState function	2025-08-04 10:59:11 +02:00
p.vanderwilt	2c9db0fcea	Fixed position and log settings	2025-07-31 14:48:39 +02:00
p.vanderwilt	5ec9319b3f	Add position field and proper logging configuration	2025-07-24 12:13:16 +02:00
p.vanderwilt	31d30c6db3	Renamed advanced-reactor to advancedReactor to prevent errors due to hyphen in name	2025-07-24 11:53:23 +02:00
p.vanderwilt	da90224d3f	Added loggin to advanced-reactor. Currently broken for some reason?	2025-07-23 17:16:35 +02:00
p.vanderwilt	ef02c47cff	Add WIP oxygen measurement child relation	2025-07-22 14:36:52 +02:00
p.vanderwilt	a2dbd468d5	Merge pull request 'Implemented parent-child relations for reactor node' (#15 ) from multi-output into main Reviewed-on: p.vanderwilt/asm3#15	2025-07-22 11:27:06 +00:00
p.vanderwilt	f81161b2d5	Process output using tick function rather than clock message	2025-07-22 12:20:29 +02:00
p.vanderwilt	57aafe3e0b	Minor optimisations	2025-07-21 17:28:09 +02:00
p.vanderwilt	b1719376cf	Rewrite reactor to source and register it properly to node object	2025-07-21 12:44:07 +02:00
p.vanderwilt	73c2b654e1	Deal with clock singal	2025-07-16 16:54:30 +02:00
p.vanderwilt	633a088483	Added handles for influent change emitter	2025-07-16 16:08:14 +02:00
p.vanderwilt	d5db1ae0a0	Added seperate process, DB and parent outputs	2025-07-16 10:57:35 +02:00
p.vanderwilt	6adf29427a	Merge pull request 'Switch temperature to Measurement node and finally fix boundary conditions properly' (#14 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#14	2025-07-11 10:44:26 +00:00
p.vanderwilt	6227bbe256	Update temperature handling in Reactor class and remove redundant setter	2025-07-11 12:27:06 +02:00
p.vanderwilt	24de5a4c9f	Add generalFunctions dependency and implement basic measurement child registration in nodeClass	2025-07-11 12:22:36 +02:00
p.vanderwilt	6fd86f71c8	Switched around Debug point and added checks for Pe and Co_D	2025-07-09 15:37:29 +02:00
p.vanderwilt	0f912b05e4	Add temperature handling	2025-07-09 10:29:54 +02:00
p.vanderwilt	0efa76fa6a	Reset speedUpFactor in Reactor class for simulation acceleration, disable debug	2025-07-08 15:41:41 +02:00
p.vanderwilt	c566766c4d	Refactor boundary condition application in Reactor_PFR class for improved clarity and efficiency	2025-07-08 15:29:55 +02:00
p.vanderwilt	6bdfa07d92	Merge pull request 'Added temperature-dependent rate calculation to ASM3 model' (#12 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#12	2025-07-08 10:15:09 +00:00
p.vanderwilt	c1e331b5f0	Add temperature theta parameters and adjust reaction rate calculations in ASM3 class	2025-07-08 11:02:39 +02:00
p.vanderwilt	5c03dddb79	Refactor boundary condition handling to use adjustable parameter alpha in advanced-reactor and specificClass	2025-07-08 10:03:03 +02:00
p.vanderwilt	01318a2d3b	Fix spelling of "Dirichlet" in advanced-reactor.html and specificClass.js	2025-07-07 14:58:52 +02:00
p.vanderwilt	01380c309f	Add boundary condition input and update reactor configuration handling	2025-07-07 14:47:50 +02:00
p.vanderwilt	c89d5b0024	Merge pull request 'Refactor code to align with other projects in EVOLV' (#7 ) from refactor into main Reviewed-on: p.vanderwilt/asm3#7	2025-07-07 10:26:46 +00:00
p.vanderwilt	302780726a	Refactor Reactor class to remove debug logs and enhance setter for influent data with conditional logging	2025-07-07 12:24:15 +02:00
p.vanderwilt	deb5269d1a	Change file structure to align with project	2025-07-07 11:59:11 +02:00
p.vanderwilt	b4ddb6b8df	Enhance documentation for ASM3 class and its parameters	2025-07-07 11:08:11 +02:00
p.vanderwilt	fe3add4007	Add debug assertions for state changes in Reactor classes	2025-07-04 17:42:31 +02:00
p.vanderwilt	a2cfb20e2c	Refactor reactor class to improve NaN handling and add utility function for NaN assertions	2025-07-04 16:28:35 +02:00
p.vanderwilt	6755f2bd28	Refactor reactor class to improve NaN handling and removed magic numbers	2025-07-04 16:03:42 +02:00
p.vanderwilt	4b49d10763	Fixed bug in NaN assertion	2025-07-04 15:48:05 +02:00
p.vanderwilt	c6b0cab067	Refactor advanced-reactor and nodeClass for improved readability and consistency	2025-07-04 15:14:03 +02:00
p.vanderwilt	3f5b0eea32	Enhance reactor class with NaN checks and refactor methods for clarity	2025-07-04 14:58:38 +02:00
p.vanderwilt	09e7072d16	Refactor documentation in nodeClass and reactor_class for clarity and consistency	2025-07-04 13:52:28 +02:00
p.vanderwilt	c239b71ad8	Refactor reactor constructors to accept a config object for improved clarity and maintainability	2025-07-04 13:16:49 +02:00
p.vanderwilt	348307d999	Add documentation	2025-07-04 13:09:20 +02:00
p.vanderwilt	530dac5c77	Refactor nodeClass to streamline configuration loading and reactor setup	2025-07-04 12:51:37 +02:00
p.vanderwilt	c23818c108	Remove unnecessary node parameter _setupClass	2025-07-04 12:16:08 +02:00
p.vanderwilt	fee6881f1b	Refactor nodeClass for to mostly allign with the standard EVOLV structure	2025-07-04 12:06:58 +02:00
p.vanderwilt	1cda956d83	Refactor Reactor class structure and include inheritance for CSTR and PFR	2025-07-04 11:42:34 +02:00
p.vanderwilt	25cd728b68	Refactor reactor node registration	2025-07-04 10:44:54 +02:00
p.vanderwilt	d0db1b416c	Remove debug messages	2025-07-04 10:01:46 +02:00
p.vanderwilt	0d12192ccc	Merge pull request 'New axial dispersion model with Generalised boundary conditions' (#6 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#6	2025-07-03 20:30:34 +00:00
p.vanderwilt	f517b7764d	Remove mistake boundary condition	2025-07-03 22:28:34 +02:00
p.vanderwilt	dcc8562dbf	Remove depreciated variable	2025-07-02 10:37:02 +02:00
p.vanderwilt	e9847607e8	Use Generalized boundary condition by Nauman and Mallikarjun 1983	2025-07-01 16:08:35 +02:00
p.vanderwilt	f4824b822c	Improved wieghted finite differencing	2025-07-01 13:04:32 +02:00
p.vanderwilt	3cc876533c	Changed the upper boundary to lower order scheme for now	2025-06-30 15:46:13 +02:00
p.vanderwilt	b2d32ba9f2	Enhance makeDoperator to support higher-order central gradient schemes and improve boundary handling	2025-06-30 12:50:02 +02:00
p.vanderwilt	8215c5ed9a	Add checks for NaN values in Reactor_PFR calculations and update hydrolysis rate calculation to handle division by zero	2025-06-28 19:19:38 +02:00
p.vanderwilt	0cc6538003	Handle division by zero in rate calculations for ASM3	2025-06-27 17:29:20 +02:00
p.vanderwilt	bb74fc86c2	Refactor dispersion and boundary condition handling in Reactor_PFR	2025-06-27 16:56:37 +02:00
p.vanderwilt	9f13229785	Fix boundary conditions in gradient and second derivative operators for Reactor_PFR	2025-06-24 16:38:07 +02:00
p.vanderwilt	2e76f733a8	Working on fixing the Derivative operators and BCs	2025-06-24 16:23:33 +02:00
p.vanderwilt	f2d94b26c5	Add dispersion setting in advanced-reactor and initialize axial dispersion to zero in Reactor_PFR	2025-06-24 13:28:45 +02:00
p.vanderwilt	c279552d7e	Merge pull request 'MVP for dispersion model' (#5 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#5	2025-06-24 10:36:09 +00:00
p.vanderwilt	6b57a46aab	Add typed input fields for reactor length and resolution in advanced-reactor, fixed NaN bug in reactor length	2025-06-24 12:32:11 +02:00
p.vanderwilt	e5c9010093	Fixed various bugs	2025-06-24 11:20:28 +02:00
p.vanderwilt	e6c1e21c16	Implement Danckwerts boundary condition in tick_fe method for Reactor_PFR	2025-06-23 17:46:55 +02:00
p.vanderwilt	70531a3a59	Add support for multiple reactor types (CSTR and PFR) with corresponding properties (Dichelet BC for now)	2025-06-23 16:58:02 +02:00
p.vanderwilt	62b034fb76	Added speed-up factor	2025-06-19 20:55:42 +02:00
p.vanderwilt	3d3304f23a	Merge pull request 'Fix outflow' (#4 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#4	2025-06-18 22:24:22 +00:00
p.vanderwilt	8d270c37c3	Merge branch 'main' into experimental	2025-06-18 22:24:02 +00:00
p.vanderwilt	85df04e215	Fix major bug in calculation of dC_out in tick_fe method to account for outflow	2025-06-19 00:16:54 +02:00
p.vanderwilt	5bd094f4a6	Prevent negative values in reactor state	2025-06-18 12:34:19 +02:00
p.vanderwilt	288cf905d1	Close volume balance and minor fixes	2025-06-18 10:25:40 +02:00
p.vanderwilt	c2caa7fb46	Merge pull request 'Implemented recirculation pump and settling tank' (#3 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#3	2025-06-17 11:03:43 +00:00
p.vanderwilt	167014a24b	Merge branch 'main' into experimental	2025-06-17 11:03:31 +00:00
p.vanderwilt	0469f678c5	Add settling basin node, fixed issue with object assignment	2025-06-17 13:00:18 +02:00
p.vanderwilt	1da7a9f602	Add optional kLa input and calculation to advanced-reactor node	2025-06-17 11:13:38 +02:00
p.vanderwilt	c8c588600c	Rixed multiplying message bug.	2025-06-16 17:52:31 +02:00
p.vanderwilt	3ba98d2362	Bug fix for now. Need to figure out how clock pulse will work.	2025-06-16 17:08:33 +02:00
p.vanderwilt	5281696a21	Add recirculation pump node with input handling and flow management	2025-06-16 16:53:07 +02:00
p.vanderwilt	d0f8ada144	Add number of inlets input handling to advanced-reactor node	2025-06-16 14:01:19 +02:00
p.vanderwilt	c5f6dcecae	Merge pull request 'Implemented node configuration and Effluent output' (#2 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#2	2025-06-13 13:37:14 +00:00
p.vanderwilt	ded9c55dc4	Merge branch 'main' into experimental	2025-06-13 13:37:02 +00:00
p.vanderwilt	5b7f7a3cef	Add effluent output handling	2025-06-13 15:31:31 +02:00
p.vanderwilt	d71698d94e	Refactor advanced-reactor node to improve input handling and initialize reactor properties	2025-06-13 15:10:57 +02:00
p.vanderwilt	05d33b7f39	Add fluid volume and initial component inputs to advanced-reactor node edit dialogue	2025-06-13 12:56:30 +02:00
p.vanderwilt	bf203c5219	Merge pull request 'Absolute MVP with hardcoded config and output via terminal' (#1 ) from experimental into main Reviewed-on: p.vanderwilt/asm3#1	2025-06-12 15:01:27 +00:00
p.vanderwilt	91482c564d	Fixed bugs and hard coded config for now.	2025-06-12 16:56:28 +02:00
p.vanderwilt	2182bed343	Fixed node not showing up in pallete.	2025-06-12 12:52:32 +02:00
p.vanderwilt	49334f59e9	Add advanced-reactor node-red implementation and update package.json references	2025-06-12 11:55:17 +02:00
p.vanderwilt	b210a71657	Fix structure and improve comments in ASM3 and Reactor_CSTR classes	2025-06-11 17:18:27 +02:00
p.vanderwilt	603a1d2283	Expand reactor class to build a simple CSTR model. Moved some functionality from asm3_class to reactor.	2025-06-11 16:24:27 +02:00
p.vanderwilt	341af6db4d	Refactor ASM3 constructor to remove state parameter and update compute_dC method to use state directly; add Reactor_CSTR class for reactor simulation with forward Euler method	2025-06-11 15:17:09 +02:00
p.vanderwilt	333efcda52	Add optional state parameter to compute_rates, improve comments, and implement compute_dC method	2025-06-05 17:23:51 +02:00
p.vanderwilt	f9bd4279aa	Add project files including package.json, package-lock.json, .gitignore	2025-06-05 16:57:31 +02:00
p.vanderwilt	6261ae9c47	Finish stoichiometric matrix calculations and include missing kinetic parameter in compute_rates	2025-06-05 16:31:28 +02:00
p.vanderwilt	c5a9a2e610	Implemented first five stoichiometric equations	2025-06-05 14:52:23 +02:00
p.vanderwilt	c2122e9537	Implemented rates in rates function	2025-06-04 17:28:52 +02:00
p.vanderwilt	6ae7b5bf53	Finished parameter objects	2025-06-04 15:19:17 +02:00
p.vanderwilt	087acf8395	added initial file (unfinised) Add ASM3 class with kinetic parameters and rate computation method	2025-06-04 14:24:12 +02:00
p.vanderwilt	558a9fdbab	Initial commit	2025-06-04 12:09:32 +00:00