From 5c41dc44a3ef605011da7c6dea6a596de36918d6 Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 15:46:43 +0100
Subject: [PATCH 1/7] Clean up unused code

---
 additional_nodes/recirculation-pump.html |   57 -
 additional_nodes/recirculation-pump.js   |   40 -
 additional_nodes/settling-basin.html     |   57 -
 additional_nodes/settling-basin.js       |   57 -
 flows/asm3_flows.json                    | 1763 ----------------------
 package-lock.json                        |  119 --
 package.json                             |    5 +-
 7 files changed, 2 insertions(+), 2096 deletions(-)
 delete mode 100644 additional_nodes/recirculation-pump.html
 delete mode 100644 additional_nodes/recirculation-pump.js
 delete mode 100644 additional_nodes/settling-basin.html
 delete mode 100644 additional_nodes/settling-basin.js
 delete mode 100644 flows/asm3_flows.json
 delete mode 100644 package-lock.json

diff --git a/additional_nodes/recirculation-pump.html b/additional_nodes/recirculation-pump.html
deleted file mode 100644
index 39a3753..0000000
--- a/additional_nodes/recirculation-pump.html
+++ /dev/null
@@ -1,57 +0,0 @@
-<script type="text/javascript">
-    RED.nodes.registerType("recirculation-pump", {
-        category: "WWTP",
-        color: "#e4a363",
-        defaults: {
-            name: { value: "" },
-            F2: { value: 0, required: true },
-            inlet: { value: 1, required: true }
-        },
-        inputs: 1,
-        outputs: 2,
-        outputLabels: ["Main effluent", "Recirculation effluent"],
-        icon: "font-awesome/fa-random",
-        label: function() {
-            return this.name || "Recirculation pump";
-        },
-        oneditprepare: function() {
-            $("#node-input-F2").typedInput({
-                type:"num",
-                types:["num"]
-            });
-            $("#node-input-inlet").typedInput({
-                type:"num",
-                types:["num"]
-            });
-        },
-        oneditsave: function() {
-            let debit = parseFloat($("#node-input-F2").typedInput("value"));
-            if (isNaN(debit) || debit < 0) {
-                RED.notify("Debit is not set correctly", {type: "error"});
-            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
-        }
-    });
-</script>
-
-<script type="text/html" data-template-name="recirculation-pump">
-    <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>
-    <div class="form-row">
-        <label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label>
-        <input type="text" id="node-input-F2" placeholder="m3 s-1">
-    </div>
-    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
-</script>
-
-<script type="text/html" data-help-name="recirculation-pump">
-    <p>Recirculation-pump for splitting streams</p>
-</script>
diff --git a/additional_nodes/recirculation-pump.js b/additional_nodes/recirculation-pump.js
deleted file mode 100644
index 2a02932..0000000
--- a/additional_nodes/recirculation-pump.js
+++ /dev/null
@@ -1,40 +0,0 @@
-module.exports = function(RED) {
-    function recirculation(config) {
-        RED.nodes.createNode(this, config);
-        var node = this;
-
-        let name = config.name;
-        let F2 = parseFloat(config.F2);
-        const inlet_F2 = parseInt(config.inlet);
-
-        node.on('input', function(msg, send, done) {
-            switch (msg.topic) {
-                case "Fluent":
-                    // conserve volume flow debit
-                    let F_in = msg.payload.F;
-                    let F1 = Math.max(F_in - F2, 0);
-                    let F2_corr = F_in < F2 ? F_in : F2;
-
-                    let msg_F1 = structuredClone(msg);
-                    msg_F1.payload.F = F1;
-
-                    let msg_F2 = {...msg};
-                    msg_F2.payload.F = F2_corr;
-                    msg_F2.payload.inlet = inlet_F2;
-
-                    send([msg_F1, msg_F2]);
-                    break;
-                case "clock":
-                    break;
-                default:
-                    console.log("Unknown topic: " + msg.topic);
-            }
-
-            if (done) {
-                done();
-            }
-        });
-
-    }
-    RED.nodes.registerType("recirculation-pump", recirculation);
-};
diff --git a/additional_nodes/settling-basin.html b/additional_nodes/settling-basin.html
deleted file mode 100644
index e8e8e8d..0000000
--- a/additional_nodes/settling-basin.html
+++ /dev/null
@@ -1,57 +0,0 @@
-<script type="text/javascript">
-    RED.nodes.registerType("settling-basin", {
-        category: "WWTP",
-        color: "#e4a363",
-        defaults: {
-            name: { value: "" },
-            TS_set: { value: 0.1, required: true },
-            inlet: { value: 1, required: true }
-        },
-        inputs: 1,
-        outputs: 2,
-        outputLabels: ["Main effluent", "Sludge effluent"],
-        icon: "font-awesome/fa-random",
-        label: function() {
-            return this.name || "Settling basin";
-        },
-        oneditprepare: function() {
-            $("#node-input-TS_set").typedInput({
-                type:"num",
-                types:["num"]
-            });
-            $("#node-input-inlet").typedInput({
-                type:"num",
-                types:["num"]
-            });
-        },
-        oneditsave: function() {
-            let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
-            if (isNaN(TS_set) || TS_set < 0) {
-                RED.notify("TS is not set correctly", {type: "error"});
-            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
-        }
-    });
-</script>
-
-<script type="text/html" data-template-name="settling-basin">
-    <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>
-    <div class="form-row">
-        <label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label>
-        <input type="text" id="node-input-TS_set" placeholder="">
-    </div>
-    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
-</script>
-
-<script type="text/html" data-help-name="settling-basin">
-    <p>Settling tank</p>
-</script>
diff --git a/additional_nodes/settling-basin.js b/additional_nodes/settling-basin.js
deleted file mode 100644
index dd3d697..0000000
--- a/additional_nodes/settling-basin.js
+++ /dev/null
@@ -1,57 +0,0 @@
-module.exports = function(RED) {
-    function settler(config) {
-        RED.nodes.createNode(this, config);
-        var node = this;
-
-        let name = config.name;
-        let TS_set = parseFloat(config.TS_set);
-        const inlet_sludge = parseInt(config.inlet);
-
-        node.on('input', function(msg, send, done) {
-            switch (msg.topic) {
-                case "Fluent":
-                    // conserve volume flow debit
-                    let F_in = msg.payload.F;
-                    let C_in = msg.payload.C;
-                    let F2 = (F_in * C_in[12]) / TS_set;
-
-                    let F1 = Math.max(F_in - F2, 0);
-                    let F2_corr = F_in < F2 ? F_in : F2;
-
-                    let msg_F1 = structuredClone(msg);
-                    msg_F1.payload.F = F1;
-                    msg_F1.payload.C[7] = 0;
-                    msg_F1.payload.C[8] = 0;
-                    msg_F1.payload.C[9] = 0;
-                    msg_F1.payload.C[10] = 0;
-                    msg_F1.payload.C[11] = 0;
-                    msg_F1.payload.C[12] = 0;
-
-                    let msg_F2 = {...msg};
-                    msg_F2.payload.F = F2_corr;
-                    if (F2_corr > 0) {
-                        msg_F2.payload.C[7] = F_in * C_in[7] / F2;
-                        msg_F2.payload.C[8] = F_in * C_in[8] / F2;
-                        msg_F2.payload.C[9] = F_in * C_in[9] / F2;
-                        msg_F2.payload.C[10] = F_in * C_in[10] / F2;
-                        msg_F2.payload.C[11] = F_in * C_in[11] / F2;
-                        msg_F2.payload.C[12] = F_in * C_in[12] / F2;
-                    }
-                    msg_F2.payload.inlet = inlet_sludge;
-
-                    send([msg_F1, msg_F2]);
-                    break;
-                case "clock":
-                    break;
-                default:
-                    console.log("Unknown topic: " + msg.topic);
-            }
-
-            if (done) {
-                done();
-            }
-        });
-
-    }
-    RED.nodes.registerType("settling-basin", settler);
-};
diff --git a/flows/asm3_flows.json b/flows/asm3_flows.json
deleted file mode 100644
index 7f6d216..0000000
--- a/flows/asm3_flows.json
+++ /dev/null
@@ -1,1763 +0,0 @@
-[
-    {
-        "id": "31bba0914516dd85",
-        "type": "tab",
-        "label": "Flow 2",
-        "disabled": true,
-        "info": "",
-        "env": []
-    },
-    {
-        "id": "0abdac5260d9553e",
-        "type": "tab",
-        "label": "Flow 1",
-        "disabled": false,
-        "info": "",
-        "env": []
-    },
-    {
-        "id": "394f713d4e71366c",
-        "type": "tab",
-        "label": "Flow 4",
-        "disabled": true,
-        "info": "",
-        "env": []
-    },
-    {
-        "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"
-        }
-    },
-    {
-        "id": "ac25cd90dc999a5a",
-        "type": "ui-base",
-        "name": "UI Name",
-        "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": "ec4a923c5ead6278",
-        "type": "ui-page",
-        "name": "Dashboard",
-        "ui": "ac25cd90dc999a5a",
-        "path": "/page1",
-        "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": "58b5e9368ec5774b",
-        "type": "ui-group",
-        "name": "Group 1",
-        "page": "ec4a923c5ead6278",
-        "width": 6,
-        "height": 1,
-        "order": -1,
-        "showTitle": true,
-        "className": "",
-        "visible": "true",
-        "disabled": "false",
-        "groupType": "default"
-    },
-    {
-        "id": "14172c57f4c6ff14",
-        "type": "ui-group",
-        "name": "Group 2",
-        "page": "ec4a923c5ead6278",
-        "width": 6,
-        "height": 1,
-        "order": -1,
-        "showTitle": true,
-        "className": "",
-        "visible": "true",
-        "disabled": "false",
-        "groupType": "default"
-    },
-    {
-        "id": "ca564642bfc5606c",
-        "type": "ui-page",
-        "name": "PFR",
-        "ui": "ac25cd90dc999a5a",
-        "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": "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": "f7803caf86a911f6",
-        "type": "inject",
-        "z": "31bba0914516dd85",
-        "name": "",
-        "props": [
-            {
-                "p": "timestamp",
-                "v": "",
-                "vt": "date"
-            },
-            {
-                "p": "topic",
-                "vt": "str"
-            }
-        ],
-        "repeat": "1",
-        "crontab": "",
-        "once": true,
-        "onceDelay": 0.1,
-        "topic": "clock",
-        "x": 200,
-        "y": 340,
-        "wires": [
-            [
-                "5266f4e09e7b919b"
-            ]
-        ]
-    },
-    {
-        "id": "98f5ffa4bed3b99f",
-        "type": "inject",
-        "z": "31bba0914516dd85",
-        "name": "Influx composition",
-        "props": [
-            {
-                "p": "payload"
-            },
-            {
-                "p": "topic",
-                "vt": "str"
-            },
-            {
-                "p": "timestamp",
-                "v": "",
-                "vt": "date"
-            }
-        ],
-        "repeat": "",
-        "crontab": "",
-        "once": true,
-        "onceDelay": "5",
-        "topic": "Fluent",
-        "payload": "{\"inlet\":0,\"F\":1000,\"C\":[0,30,100,16,0,0,5,25,75,30,0,0,125]}",
-        "payloadType": "json",
-        "x": 170,
-        "y": 260,
-        "wires": [
-            [
-                "5266f4e09e7b919b"
-            ]
-        ]
-    },
-    {
-        "id": "f1b3cffbd2d38473",
-        "type": "ui-chart",
-        "z": "31bba0914516dd85",
-        "group": "14172c57f4c6ff14",
-        "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": 1420,
-        "y": 300,
-        "wires": [
-            []
-        ]
-    },
-    {
-        "id": "fc4aa2928bdbe228",
-        "type": "function",
-        "z": "31bba0914516dd85",
-        "name": "Data_converter",
-        "func": "if (msg.topic != \"Fluent\") {\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": 1220,
-        "y": 300,
-        "wires": [
-            [
-                "f1b3cffbd2d38473"
-            ]
-        ]
-    },
-    {
-        "id": "e955d0c2d3246c4b",
-        "type": "ui-chart",
-        "z": "31bba0914516dd85",
-        "group": "58b5e9368ec5774b",
-        "name": "Anoxic reactor",
-        "label": "Anoxic reactor",
-        "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": 1040,
-        "y": 180,
-        "wires": [
-            []
-        ]
-    },
-    {
-        "id": "59f0787fadf99939",
-        "type": "function",
-        "z": "31bba0914516dd85",
-        "name": "Data_converter",
-        "func": "if (msg.topic != \"Fluent\") {\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    { \"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": 820,
-        "y": 180,
-        "wires": [
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-    "node_modules/decimal.js": {
-      "version": "10.6.0",
-      "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
-      "integrity": "sha512-YpgQiITW3JXGntzdUmyUR1V812Hn8T1YVXhCu+wO3OpS4eU9l4YdD3qjyiKdV6mvV29zapkMeD390UVEf2lkUg==",
-      "license": "MIT"
-    },
-    "node_modules/escape-latex": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz",
-      "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==",
-      "license": "MIT"
-    },
-    "node_modules/fraction.js": {
-      "version": "5.3.4",
-      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
-      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
-      "license": "MIT",
-      "engines": {
-        "node": "*"
-      },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/rawify"
-      }
-    },
-    "node_modules/generalFunctions": {
-      "version": "1.0.0",
-      "resolved": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
-      "license": "SEE LICENSE"
-    },
-    "node_modules/javascript-natural-sort": {
-      "version": "0.7.1",
-      "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",
-      "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==",
-      "license": "MIT"
-    },
-    "node_modules/mathjs": {
-      "version": "14.8.0",
-      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
-      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@babel/runtime": "^7.26.10",
-        "complex.js": "^2.2.5",
-        "decimal.js": "^10.4.3",
-        "escape-latex": "^1.2.0",
-        "fraction.js": "^5.2.1",
-        "javascript-natural-sort": "^0.7.1",
-        "seedrandom": "^3.0.5",
-        "tiny-emitter": "^2.1.0",
-        "typed-function": "^4.2.1"
-      },
-      "bin": {
-        "mathjs": "bin/cli.js"
-      },
-      "engines": {
-        "node": ">= 18"
-      }
-    },
-    "node_modules/seedrandom": {
-      "version": "3.0.5",
-      "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz",
-      "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==",
-      "license": "MIT"
-    },
-    "node_modules/tiny-emitter": {
-      "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz",
-      "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==",
-      "license": "MIT"
-    },
-    "node_modules/typed-function": {
-      "version": "4.2.1",
-      "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz",
-      "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">= 18"
-      }
-    }
-  }
-}
diff --git a/package.json b/package.json
index 4651d19..152c346 100644
--- a/package.json
+++ b/package.json
@@ -11,6 +11,7 @@
     "activated sludge",
     "wastewater",
     "biological model",
+    "EVOLV",
     "node-red"
   ],
   "license": "SEE LICENSE",
@@ -21,9 +22,7 @@
   },
   "node-red": {
     "nodes": {
-      "reactor": "reactor.js",
-      "recirculation-pump": "additional_nodes/recirculation-pump.js",
-      "settling-basin": "additional_nodes/settling-basin.js"
+      "reactor": "reactor.js"
     }
   },
   "dependencies": {

From b0dd9b6a8f0356fe37eda0785dbbf46c84eddee9 Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 15:47:18 +0100
Subject: [PATCH 2/7] Refactor ASM3 module to export ASM_CONSTANTS and update
 references in Reactor classes

---
 src/reaction_modules/asm3_class Koch.js |  9 +++++++--
 src/reaction_modules/asm3_class.js      |  9 +++++++--
 src/specificClass.js                    | 22 ++++++++++------------
 3 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/src/reaction_modules/asm3_class Koch.js b/src/reaction_modules/asm3_class Koch.js
index e5e98b3..0742afa 100644
--- a/src/reaction_modules/asm3_class Koch.js	
+++ b/src/reaction_modules/asm3_class Koch.js	
@@ -1,4 +1,9 @@
-const math = require('mathjs')
+const math = require('mathjs');
+
+const ASM_CONSTANTS = {
+  S_O_INDEX: 0,
+  NUM_SPECIES: 13
+};
 
 /**
  * ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters.
@@ -208,4 +213,4 @@ class ASM3 {
   }
 }
 
-module.exports = ASM3;
\ No newline at end of file
+module.exports = { ASM3, ASM_CONSTANTS };
\ No newline at end of file
diff --git a/src/reaction_modules/asm3_class.js b/src/reaction_modules/asm3_class.js
index d228619..dc519db 100644
--- a/src/reaction_modules/asm3_class.js
+++ b/src/reaction_modules/asm3_class.js
@@ -1,4 +1,9 @@
-const math = require('mathjs')
+const math = require('mathjs');
+
+const ASM_CONSTANTS = {
+  S_O_INDEX: 0,
+  NUM_SPECIES: 13
+};
 
 /**
  * ASM3 class for the Activated Sludge Model No. 3 (ASM3).
@@ -208,4 +213,4 @@ class ASM3 {
   }
 }
 
-module.exports = ASM3;
\ No newline at end of file
+module.exports = { ASM3, ASM_CONSTANTS };
\ No newline at end of file
diff --git a/src/specificClass.js b/src/specificClass.js
index 18ac54a..3f368e1 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -1,4 +1,4 @@
-const ASM3 = require('./reaction_modules/asm3_class.js');
+const { ASM3, ASM_CONSTANTS } = require('./reaction_modules/asm3_class.js');
 const { create, all, isArray, i } = require('mathjs');
 const { assertNoNaN } = require('./utils.js');
 const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
@@ -10,8 +10,6 @@ const mathConfig = {
 
 const math = create(all, mathConfig);
 
-const S_O_INDEX = 0;
-const NUM_SPECIES = 13;
 const BC_PADDING = 2;
 const DEBUG = false;
 const DAY2MS = 1000 * 60 * 60 * 24;
@@ -39,7 +37,7 @@ class Reactor {
     this.volume = config.volume; // fluid volume reactor [m3]
 
     this.Fs = [0]; // fluid debits per inlet [m3 d-1]
-    this.Cs_in = [Array(NUM_SPECIES).fill(0)]; // composition influents
+    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]
 
@@ -59,7 +57,7 @@ class Reactor {
     if (this.Fs.length <= i_in) {
       this.logger.debug(`Adding new inlet index ${i_in}.`);
       this.Fs.push(0);
-      this.Cs_in.push(Array(NUM_SPECIES).fill(0));
+      this.Cs_in.push(Array(ASM_CONSTANTS.NUM_SPECIES).fill(0));
       this.setInfluent = input;
     }
     this.Fs[i_in] = input.payload.F;
@@ -243,8 +241,8 @@ class Reactor_CSTR extends Reactor {
     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(NUM_SPECIES).fill(0.0);
-    transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
+    const transfer = Array(ASM_CONSTANTS.NUM_SPECIES).fill(0.0);
+    transfer[ASM_CONSTANTS.S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
 
     const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step)
     this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
@@ -273,7 +271,7 @@ class Reactor_PFR extends Reactor {
     this.alpha = config.alpha;
 
     this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
-    this.extendedState = Array.from(Array(this.n_x + 2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
+    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);
@@ -324,15 +322,15 @@ class Reactor_PFR extends Reactor {
     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(NUM_SPECIES).fill(0));
+    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][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
+        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][S_O_INDEX] = this._calcOTR(this.extendedState[i][S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
+        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
       }
     }
 
@@ -357,7 +355,7 @@ class Reactor_PFR extends Reactor {
     switch(measurementType) {
       case "quantity (oxygen)":
         let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
-        this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
+        this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
         break;
       default:
         super._updateMeasurement(measurementType, value, position, context);

From 9f060d2dd0c64f3d6e89759aefa3ec7b2096be5c Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 16:09:18 +0100
Subject: [PATCH 3/7] Refactor, minor changes and remove depreciated functions

---
 reactor.html         | 15 +--------------
 src/nodeClass.js     |  1 -
 src/specificClass.js | 24 ++++--------------------
 3 files changed, 5 insertions(+), 35 deletions(-)

diff --git a/reactor.html b/reactor.html
index cdca7c7..6825342 100644
--- a/reactor.html
+++ b/reactor.html
@@ -2,7 +2,7 @@
 
 <script type="text/javascript">
     RED.nodes.registerType("reactor", {
-        category: "WWTP",
+        category: "EVOLV",
         color: "#c4cce0",
         defaults: {
             name: { value: "" },
@@ -10,7 +10,6 @@
             volume: { value: 0., required: true },
             length: { value: 0.},
             resolution_L: { value: 0.},
-            alpha: {value: 0},
             kla: { value: null },
             
             S_O_init: { value: 0., required: true },
@@ -92,10 +91,6 @@
                     $(".PFR").show();
                 }
             });
-            $("#node-input-alpha").typedInput({
-                type:"num",
-                types:["num"]
-            })
             $("#node-input-timeStep").typedInput({
                 type:"num",
                 types:["num"]
@@ -149,13 +144,6 @@
         <label for="node-input-resolution_L"><i class="fa fa-tag"></i> Resolution</label>
         <input type="text" id="node-input-resolution_L" placeholder="#">
     </div>
-    <div class="PFR">
-        <p> Inlet boundary condition parameter &alpha; (&alpha; = 0: Danckwerts BC / &alpha; = 1: Dirichlet BC) </p>
-        <div class="form-row">
-            <label for="node-input-alpha"><i class="fa fa-tag"></i>Adjustable parameter BC</label>
-            <input type="text" id="node-input-alpha">
-        </div>
-    </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>
@@ -227,7 +215,6 @@
     <!-- Position fields will be injected here -->
     <div id="position-fields-placeholder"></div>
 
-
 </script>
 
 <script type="text/html" data-help-name="reactor">
diff --git a/src/nodeClass.js b/src/nodeClass.js
index 3abe037..cc42911 100644
--- a/src/nodeClass.js
+++ b/src/nodeClass.js
@@ -87,7 +87,6 @@ class nodeClass {
             volume: parseFloat(uiConfig.volume),
             length: parseFloat(uiConfig.length),
             resolution_L: parseInt(uiConfig.resolution_L),
-            alpha: parseFloat(uiConfig.alpha),
             kla: parseFloat(uiConfig.kla),
             initialState: [
                 parseFloat(uiConfig.S_O_init),
diff --git a/src/specificClass.js b/src/specificClass.js
index 3f368e1..793f741 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -25,7 +25,6 @@ class Reactor {
     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.upstreamReactor = null;
     this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
 
     this.upstreamReactor = null;
@@ -74,9 +73,9 @@ class Reactor {
 
   /**
    * Getter for effluent data.
-   * @returns {object} Effluent data object (msg), defaults to inlet 0.
+   * @returns {object} Effluent data object (msg).
    */
-  get getEffluent() { // getter for Effluent, defaults to inlet 0
+  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) {
@@ -268,8 +267,6 @@ class Reactor_PFR extends Reactor {
     this.d_x = this.length / this.n_x;
     this.A = this.volume / this.length; // crosssectional area [m2]
 
-    this.alpha = config.alpha;
-
     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));
 
@@ -375,7 +372,7 @@ class Reactor_PFR extends Reactor {
     } 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 = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
+        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])));
         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 {
@@ -438,17 +435,4 @@ class Reactor_PFR extends Reactor {
   }
 }
 
-module.exports = { Reactor_CSTR, Reactor_PFR };
-
-// DEBUG
-// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
-// let initial_state = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1];
-// const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
-// Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
-// Reactor.Fs[0] = 10;
-// Reactor.D = 0.01;
-// let N = 0;
-// while (N < 5000) {
-//     console.log(Reactor.tick(0.001));
-//     N += 1;
-// }
\ No newline at end of file
+module.exports = { Reactor_CSTR, Reactor_PFR };
\ No newline at end of file

From 260d04b96f3b3d477138c0e8425547bad4ba2c1e Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 16:36:51 +0100
Subject: [PATCH 4/7] Minor optimisations in code and clarification

---
 src/specificClass.js | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/specificClass.js b/src/specificClass.js
index 793f741..228d077 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -1,5 +1,5 @@
 const { ASM3, ASM_CONSTANTS } = require('./reaction_modules/asm3_class.js');
-const { create, all, isArray, i } = require('mathjs');
+const { create, all, isArray } = require('mathjs');
 const { assertNoNaN } = require('./utils.js');
 const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
 const EventEmitter = require('events');
@@ -96,7 +96,7 @@ class Reactor {
    * @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
-    let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
+    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);
   }
 
@@ -208,7 +208,7 @@ class Reactor {
       this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
     }
 
-    let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
+    const n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
     if (n_iter) {
       let n = 0;
       while (n < n_iter) {
@@ -294,7 +294,7 @@ class Reactor_PFR extends Reactor {
     super.updateState(newTime);
     // let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
     this.D = this._constrainDispersion(this.D);
-    let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
+    const Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
 
     // (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
     (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
@@ -351,7 +351,7 @@ class Reactor_PFR extends Reactor {
   _updateMeasurement(measurementType, value, position, context) {
     switch(measurementType) {
       case "quantity (oxygen)":
-        let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+        const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
         this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
         break;
       default:
@@ -366,31 +366,31 @@ class Reactor_PFR extends Reactor {
    */
   _applyBoundaryConditions() {
     if (this.upstreamReactor) {
+      // Open boundary
       for (let i = 0; i < BC_PADDING; i++) {
         this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
       }
     } else {
-      if (math.sum(this.Fs) > 0) { // Danckwerts BC
+      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])));
         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 {
-        for (let i = 0; i < BC_PADDING; i++) {
-          this.extendedState[i] = this.extendedState[BC_PADDING];
-        }
+        // Neumann BC (no flux)
+        this.extendedState.fill(this.extendedState[BC_PADDING], 0, BC_PADDING);
       }
     }
 
     if (this.downstreamReactor) {
+      // Open boundary
       for (let i = 0; i < BC_PADDING; i++) {
         this.extendedState[this.n_x+BC_PADDING+i] = this.downstreamReactor.state[i];
       }
     } else {
       // Neumann BC (no flux)
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
-      }
+      this.extendedState.fill(this.extendedState.at(-1-BC_PADDING), BC_PADDING+this.n_x);
     }
   }
 

From ffb4080f1498fb132cd74e5df5a728e065e503b1 Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Thu, 6 Nov 2025 17:24:10 +0100
Subject: [PATCH 5/7] Refactor boundary condition handling in Reactor_PFR class
 for improved clarity and efficiency

---
 src/specificClass.js | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/specificClass.js b/src/specificClass.js
index 228d077..12ba0da 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -365,11 +365,10 @@ class Reactor_PFR extends Reactor {
    *  for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
    */
   _applyBoundaryConditions() {
+    // Upstream BC
     if (this.upstreamReactor) {
       // Open boundary
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
-      }
+      this.extendedState.splice(0, BC_PADDING, ...this.upstreamReactor.state.slice(-BC_PADDING)); 
     } else {
       if (math.sum(this.Fs) > 0) {
         // Danckwerts BC
@@ -383,11 +382,10 @@ class Reactor_PFR extends Reactor {
       }
     }
 
+    // Downstream BC
     if (this.downstreamReactor) {
       // Open boundary
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[this.n_x+BC_PADDING+i] = this.downstreamReactor.state[i];
-      }
+      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);

From a106276ca6657ef1d6bca4e2b63d5e1d9f8b16df Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Fri, 7 Nov 2025 11:59:24 +0100
Subject: [PATCH 6/7] Add additional ASM constants, add other sensor handling,
 fix bug in kla model

---
 src/reaction_modules/asm3_class Koch.js |  2 ++
 src/reaction_modules/asm3_class.js      |  2 ++
 src/specificClass.js                    | 20 +++++++++++++++-----
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/reaction_modules/asm3_class Koch.js b/src/reaction_modules/asm3_class Koch.js
index 0742afa..741c3e7 100644
--- a/src/reaction_modules/asm3_class Koch.js	
+++ b/src/reaction_modules/asm3_class Koch.js	
@@ -2,6 +2,8 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 
diff --git a/src/reaction_modules/asm3_class.js b/src/reaction_modules/asm3_class.js
index dc519db..db39890 100644
--- a/src/reaction_modules/asm3_class.js
+++ b/src/reaction_modules/asm3_class.js
@@ -2,6 +2,8 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 
diff --git a/src/specificClass.js b/src/specificClass.js
index 12ba0da..05a6075 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -320,14 +320,14 @@ class Reactor_PFR extends Reactor {
     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)  * this.n_x/(this.n_x-2);
+      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);
       }
     }
 
@@ -349,10 +349,19 @@ class Reactor_PFR extends Reactor {
   }
 
   _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)":
-        const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
-        this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
+        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);
@@ -375,6 +384,7 @@ class Reactor_PFR extends Reactor {
         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
         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)

From 2b37163a8a9869b5044d63516c4dcef59d634f22 Mon Sep 17 00:00:00 2001
From: "p.vanderwilt" <p.van.der.wilt@brabantsedelta.nl>
Date: Fri, 7 Nov 2025 16:51:48 +0100
Subject: [PATCH 7/7] Minor fixes

---
 reactor.html         | 2 +-
 src/specificClass.js | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/reactor.html b/reactor.html
index 6825342..e8c57c5 100644
--- a/reactor.html
+++ b/reactor.html
@@ -31,7 +31,7 @@
             enableLog: { value: false },
             logLevel: { value: "error" },
 
-            positionVsParent: { value: "" },
+            positionVsParent: { value: "" }
         },
         inputs: 1,
         outputs: 3,
diff --git a/src/specificClass.js b/src/specificClass.js
index 05a6075..23c1289 100644
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -203,7 +203,7 @@ class Reactor {
    * 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 = Date.now()) { // expect update with timestamp
+  updateState(newTime) { // expect update with timestamp
     if (this.upstreamReactor) {
       this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
     }
@@ -320,7 +320,7 @@ class Reactor_PFR extends Reactor {
     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);