docs: add CLAUDE.md with S88 classification and superproject rule reference

References the flow-layout rule set in the EVOLV superproject (.claude/rules/node-red-flow-layout.md) so Claude Code sessions working in this repo know the S88 level, colour, and placement lane for this node. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Merge remote-tracking branch 'origin/main' into dev-Rene
2026-04-14 07:47:25 +02:00 · 2026-03-31 16:20:45 +02:00 · 2026-03-31 14:26:10 +02:00 · 2026-03-12 16:39:25 +01:00 · 2026-03-12 09:33:34 +01:00 · 2026-03-11 16:31:53 +01:00
48 changed files with 4068 additions and 2478 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -1,136 +1,136 @@
-# Logs
+# Logs
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+# Diagnostic reports (https://nodejs.org/api/report.html)
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--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -0,0 +1,23 @@
 # reactor — Claude Code context
 Biological reactor with ASM kinetics.
 Part of the [EVOLV](https://gitea.wbd-rd.nl/RnD/EVOLV) wastewater-automation platform.
 ## S88 classification
 | Level | Colour | Placement lane |
 |---|---|---|
 | **Unit** | `#50a8d9` | L4 |
 ## Flow layout rules
 When wiring this node into a multi-node demo or production flow, follow the
 placement rule set in the **EVOLV superproject**:
 > `.claude/rules/node-red-flow-layout.md` (in the EVOLV repo root)
 Key points for this node:
 - Place on lane **L4** (x-position per the lane table in the rule).
 - Stack same-level siblings vertically.
 - Parent/children sit on adjacent lanes (children one lane left, parent one lane right).
 - Wrap in a Node-RED group box coloured `#50a8d9` (Unit).
--- a/380
+++ b/380
@@ -1,190 +1,190 @@
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-the Appendix, so far this is required and reasonable, without reducing the scope of the rights granted by the Licence.
+the Appendix, so far this is required and reasonable, without reducing the scope of the rights granted by the Licence.
-New versions of the Licence will be published with a unique version number.
+New versions of the Licence will be published with a unique version number.
-All linguistic versions of this Licence, approved by the European Commission, have identical value. Parties can take
+All linguistic versions of this Licence, approved by the European Commission, have identical value. Parties can take
-advantage of the linguistic version of their choice.
+advantage of the linguistic version of their choice.
-
+
-14.Jurisdiction
+14.Jurisdiction
-Without prejudice to specific agreement between parties,
+Without prejudice to specific agreement between parties,
-— any litigation resulting from the interpretation of this License, arising between the European Union institutions,
+— any litigation resulting from the interpretation of this License, arising between the European Union institutions,
-bodies, offices or agencies, as a Licensor, and any Licensee, will be subject to the jurisdiction of the Court of Justice
+bodies, offices or agencies, as a Licensor, and any Licensee, will be subject to the jurisdiction of the Court of Justice
-of the European Union, as laid down in article 272 of the Treaty on the Functioning of the European Union,
+of the European Union, as laid down in article 272 of the Treaty on the Functioning of the European Union,
-— any litigation arising between other parties and resulting from the interpretation of this License, will be subject to
+— any litigation arising between other parties and resulting from the interpretation of this License, will be subject to
-the exclusive jurisdiction of the competent court where the Licensor resides or conducts its primary business.
+the exclusive jurisdiction of the competent court where the Licensor resides or conducts its primary business.
-
+
-15.Applicable Law
+15.Applicable Law
-Without prejudice to specific agreement between parties,
+Without prejudice to specific agreement between parties,
-— this Licence shall be governed by the law of the European Union Member State where the Licensor has his seat,
+— this Licence shall be governed by the law of the European Union Member State where the Licensor has his seat,
-resides or has his registered office,
+resides or has his registered office,
-— this licence shall be governed by Belgian law if the Licensor has no seat, residence or registered office inside
+— this licence shall be governed by Belgian law if the Licensor has no seat, residence or registered office inside
-a European Union Member State.
+a European Union Member State.
-
+
-
+
-                                                         Appendix
+                                                         Appendix
-
+
-‘Compatible Licences’ according to Article 5 EUPL are:
+‘Compatible Licences’ according to Article 5 EUPL are:
-— GNU General Public License (GPL) v. 2, v. 3
+— GNU General Public License (GPL) v. 2, v. 3
-— GNU Affero General Public License (AGPL) v. 3
+— GNU Affero General Public License (AGPL) v. 3
-— Open Software License (OSL) v. 2.1, v. 3.0
+— Open Software License (OSL) v. 2.1, v. 3.0
-— Eclipse Public License (EPL) v. 1.0
+— Eclipse Public License (EPL) v. 1.0
-— CeCILL v. 2.0, v. 2.1
+— CeCILL v. 2.0, v. 2.1
-— Mozilla Public Licence (MPL) v. 2
+— Mozilla Public Licence (MPL) v. 2
-— GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
+— GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
-— Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for works other than software
+— Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for works other than software
-— European Union Public Licence (EUPL) v. 1.1, v. 1.2
+— European Union Public Licence (EUPL) v. 1.1, v. 1.2
-— Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong Reciprocity (LiLiQ-R+).
+— Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong Reciprocity (LiLiQ-R+).
-
+
-The European Commission may update this Appendix to later versions of the above licences without producing
+The European Commission may update this Appendix to later versions of the above licences without producing
-a new version of the EUPL, as long as they provide the rights granted in Article 2 of this Licence and protect the
+a new version of the EUPL, as long as they provide the rights granted in Article 2 of this Licence and protect the
-covered Source Code from exclusive appropriation.
+covered Source Code from exclusive appropriation.
-All other changes or additions to this Appendix require the production of a new EUPL version.
+All other changes or additions to this Appendix require the production of a new EUPL version.
--- a/README.md
+++ b/README.md
@@ -1,17 +1,17 @@
-# reactor
+# reactor
-
+
-Reactor: Advanced Hydraulic Tank & Biological Process Simulator
+Reactor: Advanced Hydraulic Tank & Biological Process Simulator
-
+
-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.
+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.
-
+
-Key Features:
+Key Features:
-
+
-Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
+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)
+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
+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
+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
+Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
-Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
+Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
-Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
+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.
+Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.
-
+
--- a/additional_nodes/recirculation-pump.html
+++ b/additional_nodes/recirculation-pump.html
@@ -1,57 +1,57 @@
-<script type="text/javascript">
+<script type="text/javascript">
-    RED.nodes.registerType("recirculation-pump", {
+    RED.nodes.registerType("recirculation-pump", {
-        category: "WWTP",
+        category: "WWTP",
-        color: "#e4a363",
+        color: "#e4a363",
-        defaults: {
+        defaults: {
-            name: { value: "" },
+            name: { value: "" },
-            F2: { value: 0, required: true },
+            F2: { value: 0, required: true },
-            inlet: { value: 1, required: true }
+            inlet: { value: 1, required: true }
-        },
+        },
-        inputs: 1,
+        inputs: 1,
-        outputs: 2,
+        outputs: 2,
-        outputLabels: ["Main effluent", "Recirculation effluent"],
+        outputLabels: ["Main effluent", "Recirculation effluent"],
-        icon: "font-awesome/fa-random",
+        icon: "font-awesome/fa-random",
-        label: function() {
+        label: function() {
-            return this.name || "Recirculation pump";
+            return this.name || "Recirculation pump";
-        },
+        },
-        oneditprepare: function() {
+        oneditprepare: function() {
-            $("#node-input-F2").typedInput({
+            $("#node-input-F2").typedInput({
-                type:"num",
+                type:"num",
-                types:["num"]
+                types:["num"]
-            });
+            });
-            $("#node-input-inlet").typedInput({
+            $("#node-input-inlet").typedInput({
-                type:"num",
+                type:"num",
-                types:["num"]
+                types:["num"]
-            });
+            });
-        },
+        },
-        oneditsave: function() {
+        oneditsave: function() {
-            let debit = parseFloat($("#node-input-F2").typedInput("value"));
+            let debit = parseFloat($("#node-input-F2").typedInput("value"));
-            if (isNaN(debit) || debit < 0) {
+            if (isNaN(debit) || debit < 0) {
-                RED.notify("Debit is not set correctly", {type: "error"});
+                RED.notify("Debit is not set correctly", {type: "error"});
-            }
+            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
+            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
+            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
+                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
+            }
-        }
+        }
-    });
+    });
-</script>
+</script>
-
+
-<script type="text/html" data-template-name="recirculation-pump">
+<script type="text/html" data-template-name="recirculation-pump">
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
+        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
-        <input type="text" id="node-input-name" placeholder="Name">
+        <input type="text" id="node-input-name" placeholder="Name">
-    </div>
+    </div>
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label>
+        <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">
+        <input type="text" id="node-input-F2" placeholder="m3 s-1">
-    </div>
+    </div>
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
+        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
+        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
+    </div>
-</script>
+</script>
-
+
-<script type="text/html" data-help-name="recirculation-pump">
+<script type="text/html" data-help-name="recirculation-pump">
-    <p>Recirculation-pump for splitting streams</p>
+    <p>Recirculation-pump for splitting streams</p>
-</script>
+</script>
--- a/additional_nodes/settling-basin.html
+++ b/additional_nodes/settling-basin.html
@@ -1,57 +1,57 @@
-<script type="text/javascript">
+<script type="text/javascript">
-    RED.nodes.registerType("settling-basin", {
+    RED.nodes.registerType("settling-basin", {
-        category: "WWTP",
+        category: "WWTP",
-        color: "#e4a363",
+        color: "#e4a363",
-        defaults: {
+        defaults: {
-            name: { value: "" },
+            name: { value: "" },
-            TS_set: { value: 0.1, required: true },
+            TS_set: { value: 0.1, required: true },
-            inlet: { value: 1, required: true }
+            inlet: { value: 1, required: true }
-        },
+        },
-        inputs: 1,
+        inputs: 1,
-        outputs: 2,
+        outputs: 2,
-        outputLabels: ["Main effluent", "Sludge effluent"],
+        outputLabels: ["Main effluent", "Sludge effluent"],
-        icon: "font-awesome/fa-random",
+        icon: "font-awesome/fa-random",
-        label: function() {
+        label: function() {
-            return this.name || "Settling basin";
+            return this.name || "Settling basin";
-        },
+        },
-        oneditprepare: function() {
+        oneditprepare: function() {
-            $("#node-input-TS_set").typedInput({
+            $("#node-input-TS_set").typedInput({
-                type:"num",
+                type:"num",
-                types:["num"]
+                types:["num"]
-            });
+            });
-            $("#node-input-inlet").typedInput({
+            $("#node-input-inlet").typedInput({
-                type:"num",
+                type:"num",
-                types:["num"]
+                types:["num"]
-            });
+            });
-        },
+        },
-        oneditsave: function() {
+        oneditsave: function() {
-            let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
+            let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
-            if (isNaN(TS_set) || TS_set < 0) {
+            if (isNaN(TS_set) || TS_set < 0) {
-                RED.notify("TS is not set correctly", {type: "error"});
+                RED.notify("TS is not set correctly", {type: "error"});
-            }
+            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
+            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
+            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
+                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
+            }
-        }
+        }
-    });
+    });
-</script>
+</script>
-
+
-<script type="text/html" data-template-name="settling-basin">
+<script type="text/html" data-template-name="settling-basin">
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
+        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
-        <input type="text" id="node-input-name" placeholder="Name">
+        <input type="text" id="node-input-name" placeholder="Name">
-    </div>
+    </div>
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label>
+        <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="">
+        <input type="text" id="node-input-TS_set" placeholder="">
-    </div>
+    </div>
-    <div class="form-row">
+    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
+        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
+        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
+    </div>
-</script>
+</script>
-
+
-<script type="text/html" data-help-name="settling-basin">
+<script type="text/html" data-help-name="settling-basin">
-    <p>Settling tank</p>
+    <p>Settling tank</p>
-</script>
+</script>
--- a/examples/README.md
+++ b/examples/README.md
@@ -0,0 +1,8 @@
 # reactor Example Flows
 Import-ready Node-RED examples for reactor.
 ## Files
 - basic.flow.json
 - integration.flow.json
 - edge.flow.json
--- a/examples/basic.flow.json
+++ b/examples/basic.flow.json
@@ -0,0 +1,6 @@
 [
  {"id":"reactor_basic_tab","type":"tab","label":"reactor basic","disabled":false,"info":"reactor basic example"},
  {"id":"reactor_basic_node","type":"reactor","z":"reactor_basic_tab","name":"reactor basic","x":420,"y":180,"wires":[["reactor_basic_dbg"]]},
  {"id":"reactor_basic_inj","type":"inject","z":"reactor_basic_tab","name":"basic trigger","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"ping","payload":"1","payloadType":"str","x":160,"y":180,"wires":[["reactor_basic_node"]]},
  {"id":"reactor_basic_dbg","type":"debug","z":"reactor_basic_tab","name":"reactor basic debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
 ]
--- a/examples/edge.flow.json
+++ b/examples/edge.flow.json
@@ -0,0 +1,6 @@
 [
  {"id":"reactor_edge_tab","type":"tab","label":"reactor edge","disabled":false,"info":"reactor edge example"},
  {"id":"reactor_edge_node","type":"reactor","z":"reactor_edge_tab","name":"reactor edge","x":420,"y":180,"wires":[["reactor_edge_dbg"]]},
  {"id":"reactor_edge_inj","type":"inject","z":"reactor_edge_tab","name":"unknown topic","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"doesNotExist","payload":"x","payloadType":"str","x":170,"y":180,"wires":[["reactor_edge_node"]]},
  {"id":"reactor_edge_dbg","type":"debug","z":"reactor_edge_tab","name":"reactor edge debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":660,"y":180,"wires":[]}
 ]
--- a/examples/integration.flow.json
+++ b/examples/integration.flow.json
@@ -0,0 +1,6 @@
 [
  {"id":"reactor_int_tab","type":"tab","label":"reactor integration","disabled":false,"info":"reactor integration example"},
  {"id":"reactor_int_node","type":"reactor","z":"reactor_int_tab","name":"reactor integration","x":420,"y":180,"wires":[["reactor_int_dbg"]]},
  {"id":"reactor_int_inj","type":"inject","z":"reactor_int_tab","name":"registerChild","props":[{"p":"topic","vt":"str"},{"p":"payload","vt":"str"}],"topic":"registerChild","payload":"example-child-id","payloadType":"str","x":170,"y":180,"wires":[["reactor_int_node"]]},
  {"id":"reactor_int_dbg","type":"debug","z":"reactor_int_tab","name":"reactor integration debug","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"true","targetType":"full","x":680,"y":180,"wires":[]}
 ]
--- a/flows/asm3_flows.json
+++ b/flows/asm3_flows.json
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,119 +1,119 @@
-{
+{
-  "name": "reactor",
+  "name": "reactor",
-  "version": "0.0.1",
+  "version": "0.0.1",
-  "lockfileVersion": 3,
+  "lockfileVersion": 3,
-  "requires": true,
+  "requires": true,
-  "packages": {
+  "packages": {
-    "": {
+    "": {
-      "name": "reactor",
+      "name": "reactor",
-      "version": "0.0.1",
+      "version": "0.0.1",
-      "license": "SEE LICENSE",
+      "license": "SEE LICENSE",
-      "dependencies": {
+      "dependencies": {
-        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
+        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
-        "mathjs": "^14.5.2"
+        "mathjs": "^14.5.2"
-      }
+      }
-    },
+    },
-    "node_modules/@babel/runtime": {
+    "node_modules/@babel/runtime": {
-      "version": "7.28.4",
+      "version": "7.28.4",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
-      "integrity": "sha512-Q/N6JNWvIvPnLDvjlE1OUBLPQHH6l3CltCEsHIujp45zQUSSh8K+gHnaEX45yAT1nyngnINhvWtzN+Nb9D8RAQ==",
+      "integrity": "sha512-Q/N6JNWvIvPnLDvjlE1OUBLPQHH6l3CltCEsHIujp45zQUSSh8K+gHnaEX45yAT1nyngnINhvWtzN+Nb9D8RAQ==",
-      "license": "MIT",
+      "license": "MIT",
-      "engines": {
+      "engines": {
-        "node": ">=6.9.0"
+        "node": ">=6.9.0"
-      }
+      }
-    },
+    },
-    "node_modules/complex.js": {
+    "node_modules/complex.js": {
-      "version": "2.4.2",
+      "version": "2.4.2",
-      "resolved": "https://registry.npmjs.org/complex.js/-/complex.js-2.4.2.tgz",
+      "resolved": "https://registry.npmjs.org/complex.js/-/complex.js-2.4.2.tgz",
-      "integrity": "sha512-qtx7HRhPGSCBtGiST4/WGHuW+zeaND/6Ld+db6PbrulIB1i2Ev/2UPiqcmpQNPSyfBKraC0EOvOKCB5dGZKt3g==",
+      "integrity": "sha512-qtx7HRhPGSCBtGiST4/WGHuW+zeaND/6Ld+db6PbrulIB1i2Ev/2UPiqcmpQNPSyfBKraC0EOvOKCB5dGZKt3g==",
-      "license": "MIT",
+      "license": "MIT",
-      "engines": {
+      "engines": {
-        "node": "*"
+        "node": "*"
-      },
+      },
-      "funding": {
+      "funding": {
-        "type": "github",
+        "type": "github",
-        "url": "https://github.com/sponsors/rawify"
+        "url": "https://github.com/sponsors/rawify"
-      }
+      }
-    },
+    },
-    "node_modules/decimal.js": {
+    "node_modules/decimal.js": {
-      "version": "10.6.0",
+      "version": "10.6.0",
-      "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
+      "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
-      "integrity": "sha512-YpgQiITW3JXGntzdUmyUR1V812Hn8T1YVXhCu+wO3OpS4eU9l4YdD3qjyiKdV6mvV29zapkMeD390UVEf2lkUg==",
+      "integrity": "sha512-YpgQiITW3JXGntzdUmyUR1V812Hn8T1YVXhCu+wO3OpS4eU9l4YdD3qjyiKdV6mvV29zapkMeD390UVEf2lkUg==",
-      "license": "MIT"
+      "license": "MIT"
-    },
+    },
-    "node_modules/escape-latex": {
+    "node_modules/escape-latex": {
-      "version": "1.2.0",
+      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz",
+      "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz",
-      "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==",
+      "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==",
-      "license": "MIT"
+      "license": "MIT"
-    },
+    },
-    "node_modules/fraction.js": {
+    "node_modules/fraction.js": {
-      "version": "5.3.4",
+      "version": "5.3.4",
-      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
+      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
-      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
+      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
-      "license": "MIT",
+      "license": "MIT",
-      "engines": {
+      "engines": {
-        "node": "*"
+        "node": "*"
-      },
+      },
-      "funding": {
+      "funding": {
-        "type": "github",
+        "type": "github",
-        "url": "https://github.com/sponsors/rawify"
+        "url": "https://github.com/sponsors/rawify"
-      }
+      }
-    },
+    },
-    "node_modules/generalFunctions": {
+    "node_modules/generalFunctions": {
-      "version": "1.0.0",
+      "version": "1.0.0",
-      "resolved": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
+      "resolved": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
-      "license": "SEE LICENSE"
+      "license": "SEE LICENSE"
-    },
+    },
-    "node_modules/javascript-natural-sort": {
+    "node_modules/javascript-natural-sort": {
-      "version": "0.7.1",
+      "version": "0.7.1",
-      "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",
+      "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",
-      "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==",
+      "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==",
-      "license": "MIT"
+      "license": "MIT"
-    },
+    },
-    "node_modules/mathjs": {
+    "node_modules/mathjs": {
-      "version": "14.8.0",
+      "version": "14.8.0",
-      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
+      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
-      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
+      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
-      "license": "Apache-2.0",
+      "license": "Apache-2.0",
-      "dependencies": {
+      "dependencies": {
-        "@babel/runtime": "^7.26.10",
+        "@babel/runtime": "^7.26.10",
-        "complex.js": "^2.2.5",
+        "complex.js": "^2.2.5",
-        "decimal.js": "^10.4.3",
+        "decimal.js": "^10.4.3",
-        "escape-latex": "^1.2.0",
+        "escape-latex": "^1.2.0",
-        "fraction.js": "^5.2.1",
+        "fraction.js": "^5.2.1",
-        "javascript-natural-sort": "^0.7.1",
+        "javascript-natural-sort": "^0.7.1",
-        "seedrandom": "^3.0.5",
+        "seedrandom": "^3.0.5",
-        "tiny-emitter": "^2.1.0",
+        "tiny-emitter": "^2.1.0",
-        "typed-function": "^4.2.1"
+        "typed-function": "^4.2.1"
-      },
+      },
-      "bin": {
+      "bin": {
-        "mathjs": "bin/cli.js"
+        "mathjs": "bin/cli.js"
-      },
+      },
-      "engines": {
+      "engines": {
-        "node": ">= 18"
+        "node": ">= 18"
-      }
+      }
-    },
+    },
-    "node_modules/seedrandom": {
+    "node_modules/seedrandom": {
-      "version": "3.0.5",
+      "version": "3.0.5",
-      "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz",
+      "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz",
-      "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==",
+      "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==",
-      "license": "MIT"
+      "license": "MIT"
-    },
+    },
-    "node_modules/tiny-emitter": {
+    "node_modules/tiny-emitter": {
-      "version": "2.1.0",
+      "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz",
-      "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==",
+      "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==",
-      "license": "MIT"
+      "license": "MIT"
-    },
+    },
-    "node_modules/typed-function": {
+    "node_modules/typed-function": {
-      "version": "4.2.1",
+      "version": "4.2.1",
-      "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz",
+      "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz",
-      "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==",
+      "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==",
-      "license": "MIT",
+      "license": "MIT",
-      "engines": {
+      "engines": {
-        "node": ">= 18"
+        "node": ">= 18"
-      }
+      }
-    }
+    }
-  }
+  }
-}
+}
--- a/package.json
+++ b/package.json
@@ -1,33 +1,33 @@
-{
+{
-  "name": "reactor",
+  "name": "reactor",
-  "version": "0.0.1",
+  "version": "0.0.1",
-  "description": "Implementation of the asm3 model for Node-Red",
+  "description": "Implementation of the asm3 model for Node-Red",
-  "repository": {
+  "repository": {
-    "type": "git",
+    "type": "git",
-    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
+    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
-  },
+  },
-  "keywords": [
+  "keywords": [
-    "asm3",
+    "asm3",
-    "activated sludge",
+    "activated sludge",
-    "wastewater",
+    "wastewater",
-    "biological model",
+    "biological model",
-    "node-red"
+    "node-red"
-  ],
+  ],
-  "license": "SEE LICENSE",
+  "license": "SEE LICENSE",
-  "author": "P.R. van der Wilt",
+  "author": "P.R. van der Wilt",
-  "main": "reactor.js",
+  "main": "reactor.js",
  "scripts": {
-    "test": "node reactor.js"
+    "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js"
  },
-  "node-red": {
+  "node-red": {
-    "nodes": {
+    "nodes": {
-      "reactor": "reactor.js",
+      "reactor": "reactor.js",
-      "recirculation-pump": "additional_nodes/recirculation-pump.js",
+      "recirculation-pump": "additional_nodes/recirculation-pump.js",
-      "settling-basin": "additional_nodes/settling-basin.js"
+      "settling-basin": "additional_nodes/settling-basin.js"
-    }
+    }
-  },
+  },
-  "dependencies": {
+  "dependencies": {
-    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
+    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
-    "mathjs": "^14.5.2"
+    "mathjs": "^14.5.2"
-  }
+  }
-}
+}
--- a/reactor.html
+++ b/reactor.html
@@ -1,9 +1,19 @@
 <!--
 | S88-niveau             | Primair (blokkleur) | Tekstkleur |
 | ---------------------- | ------------------- | ---------- |
 | **Area**               | `#0f52a5`           | wit        |
 | **Process Cell**       | `#0c99d9`           | wit        |
 | **Unit**               | `#50a8d9`           | zwart      |
 | **Equipment (Module)** | `#86bbdd`           | zwart      |
 | **Control Module**     | `#a9daee`           | zwart      |
 -->
 <script src="/reactor/menu.js"></script>
 <script type="text/javascript">
    RED.nodes.registerType("reactor", {
-        category: "WWTP",
+        category: "EVOLV",
-        color: "#c4cce0",
+        color: "#50a8d9",
        defaults: {
            name: { value: "" },
            reactor_type: { value: "CSTR", required: true },
@@ -13,7 +23,7 @@
            alpha: {value: 0},
            n_inlets: { value: 1, required: true},
            kla: { value: null },
-            
+
            S_O_init: { value: 0., required: true },
            S_I_init: { value: 30., required: true },
            S_S_init: { value: 100., required: true },
@@ -29,6 +39,9 @@
            X_TS_init: { value: 125.0009, required: true },
            timeStep: { value: 1, required: true },
            speedUpFactor: { value: 1 },
            processOutputFormat: { value: "process" },
            dbaseOutputFormat: { value: "influxdb" },
            enableLog: { value: false },
            logLevel: { value: "error" },
@@ -39,7 +52,7 @@
        outputs: 3,
        inputLabels: ["input"],
        outputLabels: ["process", "dbase", "parent"],
-        icon: "font-awesome/fa-recycle",
+        icon: "font-awesome/fa-flask",
        label: function() {
            return this.name || "Reactor";
        },
@@ -105,6 +118,10 @@
                type:"num",
                types:["num"]
            })
            $("#node-input-speedUpFactor").typedInput({
                type:"num",
                types:["num"]
            })
            // Set initial visibility on dialog open
            const initialType = $("#node-input-reactor_type").typedInput("value");
            if (initialType === "CSTR") {
@@ -120,8 +137,8 @@
            }
            // save position field
-            if (window.EVOLV?.nodes?.measurement?.positionMenu?.saveEditor) {
+            if (window.EVOLV?.nodes?.reactor?.positionMenu?.saveEditor) {
-                window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
+                window.EVOLV.nodes.reactor.positionMenu.saveEditor(this);
            }
            let volume = parseFloat($("#node-input-volume").typedInput("value"));
@@ -233,6 +250,27 @@
        <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">
        <label for="node-input-speedUpFactor"><i class="fa fa-tag"></i> Speed-up factor</label>
        <input type="text" id="node-input-speedUpFactor" placeholder="1 = real-time">
    </div>
    <h3>Output Formats</h3>
    <div class="form-row">
        <label for="node-input-processOutputFormat"><i class="fa fa-random"></i> Process Output</label>
        <select id="node-input-processOutputFormat" style="width:60%;">
            <option value="process">process</option>
            <option value="json">json</option>
            <option value="csv">csv</option>
        </select>
    </div>
    <div class="form-row">
        <label for="node-input-dbaseOutputFormat"><i class="fa fa-database"></i> Database Output</label>
        <select id="node-input-dbaseOutputFormat" style="width:60%;">
            <option value="influxdb">influxdb</option>
            <option value="json">json</option>
            <option value="csv">csv</option>
        </select>
    </div>
    <!-- Logger fields injected here -->
 	<div id="logger-fields-placeholder"></div>
--- a/reactor.js
+++ b/reactor.js
@@ -1,26 +1,26 @@
-const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
+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 nodeClass = require('./src/nodeClass.js'); // node class
-const { MenuManager } = require('generalFunctions');
+const { MenuManager } = require('generalFunctions');
-
+
-
+
-module.exports = function (RED) {
+module.exports = function (RED) {
-    // Register the node type
+    // Register the node type
-    RED.nodes.registerType(nameOfNode, function (config) {
+    RED.nodes.registerType(nameOfNode, function (config) {
-        // Initialize the Node-RED node first
+        // Initialize the Node-RED node first
-        RED.nodes.createNode(this, config);
+        RED.nodes.createNode(this, config);
-        // Then create your custom class and attach it
+        // Then create your custom class and attach it
-        this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
+        this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
-    });
+    });
-
+
-    const menuMgr = new MenuManager();
+    const menuMgr = new MenuManager();
-
+
-    // Serve /advancedReactor/menu.js
+    // Serve /advancedReactor/menu.js
-    RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
+    RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
-        try {
+        try {
-            const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
+            const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
-            res.type('application/javascript').send(script);
+            res.type('application/javascript').send(script);
-        } catch (err) {
+        } catch (err) {
-            res.status(500).send(`// Error generating menu: ${err.message}`);
+            res.status(500).send(`// Error generating menu: ${err.message}`);
-        }
+        }
-    });
+    });
-};
+};
--- a/src/nodeClass.js
+++ b/src/nodeClass.js
@@ -1,5 +1,21 @@
 const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
-const { configManager } = require('generalFunctions');
+const { outputUtils, configManager } = require('generalFunctions');
 const REACTOR_SPECIES = [
    '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'
 ];
 class nodeClass {
@@ -19,6 +35,7 @@ class nodeClass {
        this._loadConfig(uiConfig)
        this._setupClass();
        this._output = new outputUtils();
        this._attachInputHandler();
        this._registerChild();
@@ -31,43 +48,49 @@ class nodeClass {
     */
    _attachInputHandler() {
        this.node.on('input', (msg, send, done) => {
-
+            try {
-            switch (msg.topic) {
+                switch (msg.topic) {
-                case "clock":
+                    case "clock":
-                    this.source.updateState(msg.timestamp);
+                        this.source.updateState(msg.timestamp);
-                    send([msg, null, null]);
+                        send([msg, null, null]);
-                    break;
+                        break;
-                case "Fluent":
+                    case "Fluent":
-                    this.source.setInfluent = msg;
+                        this.source.setInfluent = msg;
-                    break;
+                        break;
-                case "OTR":
+                    case "OTR":
-                    this.source.setOTR = msg;
+                        this.source.setOTR = msg;
-                    break;
+                        break;
-                case "Temperature":
+                    case "Temperature":
-                    this.source.setTemperature = msg;
+                        this.source.setTemperature = msg;
-                    break;
+                        break;
-                case "Dispersion":
+                    case "Dispersion":
-                    this.source.setDispersion = msg;
+                        this.source.setDispersion = msg;
-                    break;
+                        break;
-                case 'registerChild': {
+                    case 'registerChild': {
-                    // Register this node as a parent of the child node
+                        const childId = msg.payload;
-                    const childId = msg.payload;
+                        const childObj = this.RED.nodes.getNode(childId);
-                    const childObj = this.RED.nodes.getNode(childId);
+                        if (!childObj || !childObj.source) {
-                    this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
+                            this.source?.logger?.warn(`registerChild skipped: missing child/source for id=${childId}`);
-                    break;
+                            break;
                        }
                        this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
                        break;
                    }
                    default:
                        this.source?.logger?.warn(`Unknown topic: ${msg.topic}`);
                }
-                default:
+            } catch (error) {
-                    console.log("Unknown topic: " + msg.topic);
+                this.source?.logger?.error(`Input handler failure: ${error.message}`);
            }
-            if (done) {
+            if (typeof done === 'function') {
                done();
            }
        });
    }
    /**
-     * Parse node configuration
+     * Parse node configuration using ConfigManager
     * @param {object} uiConfig Config set in UI in node-red
     */
    _loadConfig(uiConfig) {
@@ -97,7 +120,8 @@ class nodeClass {
                parseFloat(uiConfig.X_A_init),
                parseFloat(uiConfig.X_TS_init)
            ],
-            timeStep: parseFloat(uiConfig.timeStep)
+            timeStep: parseFloat(uiConfig.timeStep),
            speedUpFactor: Number(uiConfig.speedUpFactor) || 1
        });
    }
@@ -129,7 +153,8 @@ class nodeClass {
                new_reactor = new Reactor_PFR(this.config);
                break;
            default:
-                console.warn("Unknown reactor type: " + this.config.reactor_type);
+                this.node.warn("Unknown reactor type: " + this.config.reactor_type + ". Falling back to CSTR.");
                new_reactor = new Reactor_CSTR(this.config);
        }
        this.source = new_reactor; // protect from reassignment
@@ -143,15 +168,41 @@ class nodeClass {
    }
    _tick(){
-        this.node.send([this.source.getEffluent, null, null]);
+        const gridProfile = this.source.getGridProfile;
        if (gridProfile) {
            this.node.send([{ topic: "GridProfile", payload: gridProfile }, null, null]);
        }
        this.node.send([this.source.getEffluent, this._buildTelemetryMessage(), null]);
    }
    _buildTelemetryMessage() {
        const effluent = this.source?.getEffluent;
        const concentrations = effluent?.payload?.C;
        if (!Array.isArray(concentrations)) {
            return null;
        }
        const telemetry = {
            flow_total: Number(effluent.payload.F),
            temperature: Number(this.source?.temperature),
        };
        for (let i = 0; i < Math.min(REACTOR_SPECIES.length, concentrations.length); i += 1) {
            const value = Number(concentrations[i]);
            if (Number.isFinite(value)) {
                telemetry[REACTOR_SPECIES[i]] = value;
            }
        }
        return this._output.formatMsg(telemetry, this.config, 'influxdb');
    }
    _attachCloseHandler() {
        this.node.on('close', (done) => {
            clearInterval(this._tickInterval);
-            done();
+            if (typeof done === 'function') done();
        });
    }
 }
-module.exports = nodeClass;
+module.exports = nodeClass;
--- a/src/reaction_modules/asm3_class
+++ b/src/reaction_modules/asm3_class
@@ -13,13 +13,13 @@ class ASM3 {
    this.kin_params = {
      // 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] 
+      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:      10.0, // saturation constant S_s        [g COD 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]
@@ -30,7 +30,7 @@ class ASM3 {
      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_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]
@@ -132,7 +132,7 @@ class ASM3 {
  /**
   * 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. 
+   * @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) {
@@ -187,12 +187,12 @@ class ASM3 {
    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;
  }
@@ -208,4 +208,4 @@ class ASM3 {
  }
 }
-module.exports = ASM3;
+module.exports = ASM3;
--- a/src/reaction_modules/asm3_class.js
+++ b/src/reaction_modules/asm3_class.js
@@ -13,7 +13,7 @@ class ASM3 {
    this.kin_params = {
      // 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] 
+      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        [-]
@@ -30,7 +30,7 @@ class ASM3 {
      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_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]
@@ -132,7 +132,7 @@ class ASM3 {
  /**
   * 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. 
+   * @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) {
@@ -187,12 +187,12 @@ class ASM3 {
    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;
  }
@@ -208,4 +208,4 @@ class ASM3 {
  }
 }
-module.exports = ASM3;
+module.exports = ASM3;
--- a/src/specificClass.js
+++ b/src/specificClass.js
@@ -41,7 +41,7 @@ class Reactor {
    this.currentTime = Date.now(); // milliseconds since epoch [ms]
    this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
-    this.speedUpFactor = 60; // speed up factor for simulation, 60 means 1 minute per simulated second
+    this.speedUpFactor = config.speedUpFactor ?? 1; // speed up factor for simulation
  }
  /**
@@ -62,6 +62,24 @@ class Reactor {
    this.OTR = input.payload;
  }
  /**
   * Setter for reactor temperature [C].
   * Accepts either a direct numeric payload or { value } object payload.
   * @param {object} input - Input object (msg)
   */
  set setTemperature(input) {
    const payload = input?.payload;
    const rawValue = (payload && typeof payload === 'object' && payload.value !== undefined)
      ? payload.value
      : payload;
    const parsedValue = Number(rawValue);
    if (!Number.isFinite(parsedValue)) {
      this.logger.warn(`Invalid temperature input: ${rawValue}`);
      return;
    }
    this.temperature = parsedValue;
  }
  /**
   * Getter for effluent data.
   * @returns {object} Effluent data object (msg), defaults to inlet 0.
@@ -73,6 +91,8 @@ class Reactor {
    return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
  }
  get getGridProfile() { return null; }
  /**
   * 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].
@@ -84,6 +104,29 @@ class Reactor {
    return this.kla * (S_O_sat - S_O);
  }
  _calcOxygenSaturation(T = 20.0) {
    return 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
  }
  _capDissolvedOxygen(state) {
    const saturation = this._calcOxygenSaturation(this.temperature);
    const capRow = (row) => {
      if (!Array.isArray(row)) {
        return row;
      }
      const next = row.slice();
      if (Number.isFinite(next[S_O_INDEX])) {
        next[S_O_INDEX] = Math.max(0, Math.min(next[S_O_INDEX], saturation));
      }
      return next;
    };
    if (Array.isArray(state) && Array.isArray(state[0])) {
      return state.map(capRow);
    }
    return capRow(state);
  }
  /**
   * Clip values in an array to zero.
   * @param {Array} arr - Array of values to clip.
@@ -138,7 +181,7 @@ class Reactor {
        .variant("measured")
        .position(position)
        .value(eventData.value, eventData.timestamp, eventData.unit);
-      
+
      this._updateMeasurement(measurementType, eventData.value, position, eventData);
    });
  }
@@ -158,7 +201,7 @@ class Reactor {
    });
  }
-  
+
  _updateMeasurement(measurementType, value, position, _context) {
    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
    switch (measurementType) {
@@ -220,7 +263,7 @@ class Reactor_CSTR extends Reactor {
    transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
    const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step)
-    this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
+    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(math.add(this.state, dC_total))); // clip concentrations and enforce physical DO saturation
    if(DEBUG){
      assertNoNaN(dC_total, "change in state");
      assertNoNaN(this.state, "new state");
@@ -256,6 +299,18 @@ class Reactor_PFR extends Reactor {
    assertNoNaN(this.D2_op, "Second derivative operator");
  }
  get getGridProfile() {
    return {
      grid: this.state.map(row => row.slice()),
      n_x: this.n_x,
      d_x: this.d_x,
      length: this.length,
      species: ['S_O','S_I','S_S','S_NH','S_N2','S_NO','S_HCO',
                'X_I','X_S','X_H','X_STO','X_A','X_TS'],
      timestamp: this.currentTime
    };
  }
  /**
   * Setter for axial dispersion.
   * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
@@ -269,7 +324,7 @@ class Reactor_PFR extends Reactor {
    let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
    let Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
-    (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
+    (Pe_local >= 2) && this.logger.warn(`Local Peclet 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.`);
    if(DEBUG) {
@@ -315,19 +370,26 @@ class Reactor_PFR extends Reactor {
      assertNoNaN(stateNew, "new state post BC");
    }
-    this.state = this._arrayClip2Zero(stateNew);
+    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
    return stateNew;
  }
-  _updateMeasurement(measurementType, value, position, _context) {
+  _updateMeasurement(measurementType, value, position, context) {
    switch(measurementType) {
-      case "quantity (oxygen)": {
+      case "quantity (oxygen)":
-        let grid_pos = Math.round(position / this.config.length * this.n_x);
+        if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) {
-        this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
+          this.logger.warn(`Ignoring oxygen measurement update with invalid data (position=${position}, value=${value}).`);
          break;
        }
        {
          // Clamp sensor-derived position to valid PFR grid bounds.
          const rawIndex = Math.round(position / this.config.length * this.n_x);
          const grid_pos = Math.max(0, Math.min(this.n_x - 1, rawIndex));
          this.state[grid_pos][S_O_INDEX] = value; // reconcile measured oxygen concentration into nearest grid cell
        }
        break;
      }
      default:
-        super._updateMeasurement(measurementType, value, position, _context);
+        super._updateMeasurement(measurementType, value, position, context);
    }
  }
@@ -416,4 +478,4 @@ module.exports = { Reactor_CSTR, Reactor_PFR };
 // while (N < 5000) {
 //     console.log(Reactor.tick(0.001));
 //     N += 1;
-// }
+// }
--- a/src/utils.js
+++ b/src/utils.js
@@ -1,18 +1,18 @@
-/**
+/**
- * Assert that no NaN values are present in an array.
+ * Assert that no NaN values are present in an array.
- * @param {Array} arr 
+ * @param {Array} arr 
- * @param {string} label 
+ * @param {string} label 
- */
+ */
-function assertNoNaN(arr, label = "array") {
+function assertNoNaN(arr, label = "array") {
-    if (Array.isArray(arr)) {
+    if (Array.isArray(arr)) {
-        for (const el of arr) {
+        for (const el of arr) {
-            assertNoNaN(el, label);
+            assertNoNaN(el, label);
-        }
+        }
-    } else {
+    } else {
-        if (Number.isNaN(arr)) {
+        if (Number.isNaN(arr)) {
-            throw new Error(`NaN detected in ${label}!`);
+            throw new Error(`NaN detected in ${label}!`);
-        }
+        }
-    }
+    }
-}
+}
-
+
 module.exports = { assertNoNaN };
--- a/test/README.md
+++ b/test/README.md
@@ -0,0 +1,12 @@
 # reactor Test Suite Layout
 Required EVOLV layout:
 - basic/
 - integration/
 - edge/
 - helpers/
 Baseline structure tests:
 - basic/structure-module-load.basic.test.js
 - integration/structure-examples.integration.test.js
 - edge/structure-examples-node-type.edge.test.js
--- a/test/basic/.gitkeep
+++ b/test/basic/.gitkeep
--- a/test/basic/constructor.basic.test.js
+++ b/test/basic/constructor.basic.test.js
@@ -0,0 +1,55 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
 const { makeUiConfig, makeReactorConfig, makeNodeStub } = require('../helpers/factories');
 test('_loadConfig coerces numeric fields and builds initial state vector', () => {
  const inst = Object.create(NodeClass.prototype);
  inst.node = { id: 'n-reactor-1' };
  inst.name = 'reactor';
  inst._loadConfig(
    makeUiConfig({
      volume: '12.5',
      length: '9',
      resolution_L: '7',
      alpha: '0.5',
      n_inlets: '3',
      timeStep: '2',
      S_O_init: '1.1',
    }),
  );
  assert.equal(inst.config.volume, 12.5);
  assert.equal(inst.config.length, 9);
  assert.equal(inst.config.resolution_L, 7);
  assert.equal(inst.config.alpha, 0.5);
  assert.equal(inst.config.n_inlets, 3);
  assert.equal(inst.config.timeStep, 2);
  assert.equal(inst.config.initialState.length, 13);
  assert.equal(inst.config.initialState[0], 1.1);
 });
 test('_setupClass selects Reactor_CSTR when configured as CSTR', () => {
  const inst = Object.create(NodeClass.prototype);
  inst.node = makeNodeStub();
  inst.config = makeReactorConfig({ reactor_type: 'CSTR' });
  inst._setupClass();
  assert.ok(inst.source instanceof Reactor_CSTR);
  assert.equal(inst.node.source, inst.source);
 });
 test('_setupClass selects Reactor_PFR when configured as PFR', () => {
  const inst = Object.create(NodeClass.prototype);
  inst.node = makeNodeStub();
  inst.config = makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5 });
  inst._setupClass();
  assert.ok(inst.source instanceof Reactor_PFR);
  assert.equal(inst.node.source, inst.source);
 });
--- a/test/basic/cstr-tick.basic.test.js
+++ b/test/basic/cstr-tick.basic.test.js
@@ -0,0 +1,42 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 const NUM_SPECIES = 13;
 test('Reactor_CSTR tick clips negative concentrations to zero', () => {
  const reactor = new Reactor_CSTR(
    makeReactorConfig({
      reactor_type: 'CSTR',
      volume: 1,
      n_inlets: 1,
      kla: NaN,
      S_O_init: 0.1,
      S_I_init: 0.1,
      S_S_init: 0.1,
      S_NH_init: 0.1,
      S_N2_init: 0.1,
      S_NO_init: 0.1,
      S_HCO_init: 0.1,
      X_I_init: 0.1,
      X_S_init: 0.1,
      X_H_init: 0.1,
      X_STO_init: 0.1,
      X_A_init: 0.1,
      X_TS_init: 0.1,
    }),
  );
  reactor.asm = {
    compute_dC: () => Array(NUM_SPECIES).fill(0),
  };
  reactor.Fs[0] = 1;
  reactor.Cs_in[0] = Array(NUM_SPECIES).fill(0);
  reactor.tick(1);
  assert.equal(reactor.state.every((v) => Number.isFinite(v) && v >= 0), true);
  assert.equal(reactor.state.every((v) => v === 0), true);
 });
--- a/test/basic/effluent-shape.basic.test.js
+++ b/test/basic/effluent-shape.basic.test.js
@@ -0,0 +1,38 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 test('CSTR getEffluent returns flat concentration vector', () => {
  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
  reactor.state = Array.from({ length: 13 }, (_, i) => i + 1);
  reactor.Fs[0] = 5;
  const effluent = reactor.getEffluent;
  assert.equal(effluent.topic, 'Fluent');
  assert.equal(effluent.payload.inlet, 0);
  assert.equal(effluent.payload.F, 5);
  assert.deepEqual(effluent.payload.C, reactor.state);
 });
 test('PFR getEffluent returns last slice concentration vector', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 4 }),
  );
  reactor.state = [
    Array(13).fill(10),
    Array(13).fill(20),
    Array(13).fill(30),
    Array(13).fill(40),
  ];
  reactor.Fs[0] = 7;
  const effluent = reactor.getEffluent;
  assert.equal(effluent.topic, 'Fluent');
  assert.equal(effluent.payload.F, 7);
  assert.deepEqual(effluent.payload.C, Array(13).fill(40));
 });
--- a/test/basic/grid-profile.basic.test.js
+++ b/test/basic/grid-profile.basic.test.js
@@ -0,0 +1,45 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 test('CSTR getGridProfile returns null', () => {
  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
  assert.equal(reactor.getGridProfile, null);
 });
 test('PFR getGridProfile returns state matrix with correct dimensions', () => {
  const n_x = 8;
  const length = 40;
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', resolution_L: n_x, length }),
  );
  const profile = reactor.getGridProfile;
  assert.notEqual(profile, null);
  assert.equal(profile.n_x, n_x);
  assert.equal(profile.d_x, length / n_x);
  assert.equal(profile.length, length);
  assert.equal(profile.grid.length, n_x, 'grid should have n_x rows');
  assert.equal(profile.grid[0].length, 13, 'each row should have 13 species');
  assert.ok(Array.isArray(profile.species), 'species list should be an array');
  assert.equal(profile.species.length, 13);
  assert.equal(profile.species[3], 'S_NH');
  assert.equal(typeof profile.timestamp, 'number');
 });
 test('PFR getGridProfile is mutation-safe', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', resolution_L: 5, length: 10 }),
  );
  const profile = reactor.getGridProfile;
  const originalValue = reactor.state[0][3]; // S_NH at cell 0
  // Mutate the returned grid
  profile.grid[0][3] = 999;
  // Reactor internal state should be unchanged
  assert.equal(reactor.state[0][3], originalValue, 'mutating grid copy must not affect reactor state');
 });
--- a/test/basic/input-routing.basic.test.js
+++ b/test/basic/input-routing.basic.test.js
@@ -0,0 +1,77 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 test('_attachInputHandler routes supported topics to source methods/setters', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  const calls = [];
  const source = {
    updateState(timestamp) {
      calls.push(['clock', timestamp]);
    },
    childRegistrationUtils: {
      registerChild(childSource, position) {
        calls.push(['registerChild', childSource, position]);
      },
    },
  };
  Object.defineProperty(source, 'setInfluent', {
    set(v) {
      calls.push(['Fluent', v]);
    },
  });
  Object.defineProperty(source, 'setOTR', {
    set(v) {
      calls.push(['OTR', v]);
    },
  });
  Object.defineProperty(source, 'setTemperature', {
    set(v) {
      calls.push(['Temperature', v]);
    },
  });
  Object.defineProperty(source, 'setDispersion', {
    set(v) {
      calls.push(['Dispersion', v]);
    },
  });
  inst.node = node;
  inst.RED = makeREDStub({
    childA: {
      source: { id: 'child-source-A' },
    },
  });
  inst.source = source;
  inst._attachInputHandler();
  const onInput = node._handlers.input;
  const sent = [];
  let doneCount = 0;
  onInput({ topic: 'clock', timestamp: 1000 }, (msg) => sent.push(msg), () => doneCount++);
  onInput({ topic: 'Fluent', payload: { inlet: 0, F: 10, C: [] } }, () => {}, () => doneCount++);
  onInput({ topic: 'OTR', payload: 3.5 }, () => {}, () => doneCount++);
  onInput({ topic: 'Temperature', payload: 18.2 }, () => {}, () => doneCount++);
  onInput({ topic: 'Dispersion', payload: 0.2 }, () => {}, () => doneCount++);
  onInput({ topic: 'registerChild', payload: 'childA', positionVsParent: 'upstream' }, () => {}, () => doneCount++);
  assert.equal(doneCount, 6);
  assert.equal(sent.length, 1);
  assert.equal(Array.isArray(sent[0]), true);
  assert.deepEqual(calls[0], ['clock', 1000]);
  assert.equal(calls.some((x) => x[0] === 'Fluent'), true);
  assert.equal(calls.some((x) => x[0] === 'OTR'), true);
  assert.equal(calls.some((x) => x[0] === 'Temperature'), true);
  assert.equal(calls.some((x) => x[0] === 'Dispersion'), true);
  assert.deepEqual(calls.at(-1), ['registerChild', { id: 'child-source-A' }, 'upstream']);
 });
--- a/test/basic/pfr-operators.basic.test.js
+++ b/test/basic/pfr-operators.basic.test.js
@@ -0,0 +1,27 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 test('Reactor_PFR derivative operators have expected dimensions and boundary rows', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({
      reactor_type: 'PFR',
      length: 12,
      resolution_L: 6,
      volume: 60,
      n_inlets: 1,
    }),
  );
  assert.equal(reactor.D_op.length, reactor.n_x);
  assert.equal(reactor.D2_op.length, reactor.n_x);
  assert.equal(reactor.D_op.every((row) => row.length === reactor.n_x), true);
  assert.equal(reactor.D2_op.every((row) => row.length === reactor.n_x), true);
  assert.deepEqual(reactor.D_op[0], Array(reactor.n_x).fill(0));
  assert.deepEqual(reactor.D_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
  assert.deepEqual(reactor.D2_op[0], Array(reactor.n_x).fill(0));
  assert.deepEqual(reactor.D2_op[reactor.n_x - 1], Array(reactor.n_x).fill(0));
 });
--- a/test/basic/register-child.basic.test.js
+++ b/test/basic/register-child.basic.test.js
@@ -0,0 +1,39 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub } = require('../helpers/factories');
 test('_registerChild emits delayed registration message on output 2', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  inst.node = node;
  inst.config = {
    functionality: {
      positionVsParent: 'downstream',
    },
  };
  const originalSetTimeout = global.setTimeout;
  const delays = [];
  global.setTimeout = (fn, ms) => {
    delays.push(ms);
    fn();
    return 1;
  };
  try {
    inst._registerChild();
  } finally {
    global.setTimeout = originalSetTimeout;
  }
  assert.deepEqual(delays, [100]);
  assert.equal(node._sent.length, 1);
  assert.equal(Array.isArray(node._sent[0]), true);
  assert.equal(node._sent[0][2].topic, 'registerChild');
  assert.equal(node._sent[0][2].payload, node.id);
  assert.equal(node._sent[0][2].positionVsParent, 'downstream');
 });
--- a/test/basic/speedup-factor.basic.test.js
+++ b/test/basic/speedup-factor.basic.test.js
@@ -0,0 +1,68 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR } = require('../../src/specificClass');
 const nodeClass = require('../../src/nodeClass');
 const { makeReactorConfig, makeUiConfig, makeNodeStub, makeREDStub } = require('../helpers/factories');
 /**
 * Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
 */
 test('specificClass defaults speedUpFactor to 1 when not in config', () => {
  const config = makeReactorConfig();
  const reactor = new Reactor_CSTR(config);
  assert.equal(reactor.speedUpFactor, 1, 'speedUpFactor should default to 1');
 });
 test('specificClass accepts speedUpFactor from config', () => {
  const config = makeReactorConfig();
  config.speedUpFactor = 10;
  const reactor = new Reactor_CSTR(config);
  assert.equal(reactor.speedUpFactor, 10, 'speedUpFactor should be read from config');
 });
 test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () => {
  const config = makeReactorConfig();
  config.speedUpFactor = 60;
  const reactor = new Reactor_CSTR(config);
  assert.equal(reactor.speedUpFactor, 60, 'speedUpFactor=60 should be accepted');
 });
 test('nodeClass passes speedUpFactor from uiConfig to reactor config', () => {
  const uiConfig = makeUiConfig({ speedUpFactor: 5 });
  const node = makeNodeStub();
  const RED = makeREDStub();
  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
  assert.equal(nc.source.speedUpFactor, 5, 'nodeClass should pass speedUpFactor=5 to specificClass');
 });
 test('nodeClass defaults speedUpFactor to 1 when not in uiConfig', () => {
  const uiConfig = makeUiConfig();
  // Ensure speedUpFactor is not set
  delete uiConfig.speedUpFactor;
  const node = makeNodeStub();
  const RED = makeREDStub();
  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
  assert.equal(nc.source.speedUpFactor, 1, 'nodeClass should default speedUpFactor to 1');
 });
 test('updateState with speedUpFactor=1 advances roughly real-time', () => {
  const config = makeReactorConfig();
  config.speedUpFactor = 1;
  config.n_inlets = 1;
  const reactor = new Reactor_CSTR(config);
  // Set a known start time
  const t0 = reactor.currentTime;
  // Advance by 2 seconds real time
  reactor.updateState(t0 + 2000);
  // With speedUpFactor=1, simulation should have advanced ~2 seconds worth
  // (not 120 seconds like with the old hardcoded 60x factor)
  const elapsed = reactor.currentTime - t0;
  assert.ok(elapsed < 5000, `Elapsed ${elapsed}ms should be close to 2000ms, not 120000ms (old 60x factor)`);
 });
--- a/test/basic/structure-module-load.basic.test.js
+++ b/test/basic/structure-module-load.basic.test.js
@@ -0,0 +1,8 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 test('reactor module load smoke', () => {
  assert.doesNotThrow(() => {
    require('../../reactor.js');
  });
 });
--- a/test/edge/.gitkeep
+++ b/test/edge/.gitkeep
--- a/test/edge/invalid-reactor-type.edge.test.js
+++ b/test/edge/invalid-reactor-type.edge.test.js
@@ -0,0 +1,15 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub, makeUiConfig } = require('../helpers/factories');
 test('_setupClass with unknown reactor_type throws (known error-path behavior)', () => {
  const inst = Object.create(NodeClass.prototype);
  inst.node = makeNodeStub();
  inst.config = makeUiConfig({ reactor_type: 'UNKNOWN_TYPE' });
  assert.throws(() => {
    inst._setupClass();
  });
 });
--- a/test/edge/invalid-topic.edge.test.js
+++ b/test/edge/invalid-topic.edge.test.js
@@ -0,0 +1,30 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 test('unknown input topic does not throw and still calls done', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  inst.node = node;
  inst.RED = makeREDStub();
  inst.source = {
    childRegistrationUtils: {
      registerChild() {},
    },
    updateState() {},
  };
  inst._attachInputHandler();
  let doneCalled = 0;
  assert.doesNotThrow(() => {
    node._handlers.input({ topic: 'somethingUnknown', payload: 1 }, () => {}, () => {
      doneCalled += 1;
    });
  });
  assert.equal(doneCalled, 1);
 });
--- a/test/edge/missing-child.edge.test.js
+++ b/test/edge/missing-child.edge.test.js
@@ -0,0 +1,28 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub, makeREDStub } = require('../helpers/factories');
 test('registerChild with unknown node id is ignored without throwing', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  inst.node = node;
  inst.RED = makeREDStub();
  inst.source = {
    childRegistrationUtils: {
      registerChild() {},
    },
  };
  inst._attachInputHandler();
  assert.doesNotThrow(() => {
    node._handlers.input(
      { topic: 'registerChild', payload: 'missing-child', positionVsParent: 'upstream' },
      () => {},
      () => {},
    );
  });
 });
--- a/test/edge/pfr-measurement-grid.edge.test.js
+++ b/test/edge/pfr-measurement-grid.edge.test.js
@@ -0,0 +1,16 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 test('oxygen measurement at exact reactor length is clamped to the last PFR grid index', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, n_inlets: 1 }),
  );
  assert.doesNotThrow(() => {
    reactor._updateMeasurement('quantity (oxygen)', 2.5, 10, {});
  });
  assert.equal(reactor.state[reactor.n_x - 1][0], 2.5);
 });
--- a/test/edge/structure-examples-node-type.edge.test.js
+++ b/test/edge/structure-examples-node-type.edge.test.js
@@ -0,0 +1,11 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('node:fs');
 const path = require('node:path');
 const flow = JSON.parse(fs.readFileSync(path.resolve(__dirname, '../../examples/basic.flow.json'), 'utf8'));
 test('basic example includes node type reactor', () => {
  const count = flow.filter((n) => n && n.type === 'reactor').length;
  assert.equal(count >= 1, true);
 });
--- a/test/edge/zero-dispersion.edge.test.js
+++ b/test/edge/zero-dispersion.edge.test.js
@@ -0,0 +1,27 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 const DAY_MS = 1000 * 60 * 60 * 24;
 test('updateState warns when local Peclet number is too high at zero dispersion', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', length: 10, resolution_L: 5, volume: 50, n_inlets: 1 }),
  );
  const warnings = [];
  reactor.logger.warn = (msg) => warnings.push(String(msg));
  reactor.currentTime = 0;
  reactor.timeStep = 1;
  reactor.speedUpFactor = 1;
  reactor.Fs[0] = 2;
  reactor.D = 0;
  reactor.tick = () => reactor.state;
  reactor.updateState(DAY_MS);
  assert.equal(warnings.some((w) => w.includes('Péclet number') || w.includes('Peclet number')), true);
 });
--- a/test/helpers/.gitkeep
+++ b/test/helpers/.gitkeep
--- a/test/helpers/factories.js
+++ b/test/helpers/factories.js
@@ -0,0 +1,149 @@
 const EventEmitter = require('node:events');
 function makeUiConfig(overrides = {}) {
  return {
    name: 'reactor-test',
    reactor_type: 'CSTR',
    volume: 100,
    length: 10,
    resolution_L: 5,
    alpha: 0,
    n_inlets: 1,
    kla: NaN,
    S_O_init: 0,
    S_I_init: 30,
    S_S_init: 100,
    S_NH_init: 16,
    S_N2_init: 0,
    S_NO_init: 0,
    S_HCO_init: 5,
    X_I_init: 25,
    X_S_init: 75,
    X_H_init: 30,
    X_STO_init: 0,
    X_A_init: 0.001,
    X_TS_init: 125,
    timeStep: 1,
    enableLog: false,
    logLevel: 'error',
    positionVsParent: 'atEquipment',
    ...overrides,
  };
 }
 function makeReactorConfig(overrides = {}) {
  const ui = makeUiConfig(overrides);
  return {
    general: {
      id: 'reactor-node-1',
      name: ui.name,
      unit: null,
      logging: {
        enabled: ui.enableLog,
        logLevel: ui.logLevel,
      },
    },
    functionality: {
      positionVsParent: ui.positionVsParent || 'atEquipment',
      softwareType: 'reactor',
    },
    reactor_type: ui.reactor_type,
    volume: Number(ui.volume),
    length: Number(ui.length),
    resolution_L: Number(ui.resolution_L),
    alpha: Number(ui.alpha),
    n_inlets: Number(ui.n_inlets),
    kla: Number(ui.kla),
    initialState: [
      Number(ui.S_O_init),
      Number(ui.S_I_init),
      Number(ui.S_S_init),
      Number(ui.S_NH_init),
      Number(ui.S_N2_init),
      Number(ui.S_NO_init),
      Number(ui.S_HCO_init),
      Number(ui.X_I_init),
      Number(ui.X_S_init),
      Number(ui.X_H_init),
      Number(ui.X_STO_init),
      Number(ui.X_A_init),
      Number(ui.X_TS_init),
    ],
    timeStep: Number(ui.timeStep),
  };
 }
 function makeNodeStub() {
  const handlers = {};
  const sent = [];
  const warns = [];
  const errors = [];
  const statuses = [];
  return {
    id: 'reactor-node-1',
    source: null,
    on(event, cb) {
      handlers[event] = cb;
    },
    send(msg) {
      sent.push(msg);
    },
    warn(msg) {
      warns.push(msg);
    },
    error(msg) {
      errors.push(msg);
    },
    status(msg) {
      statuses.push(msg);
    },
    _handlers: handlers,
    _sent: sent,
    _warns: warns,
    _errors: errors,
    _statuses: statuses,
  };
 }
 function makeREDStub(nodeMap = {}) {
  return {
    nodes: {
      getNode(id) {
        return nodeMap[id] || null;
      },
      createNode() {},
      registerType() {},
    },
    httpAdmin: {
      get() {},
    },
  };
 }
 function makeMeasurementChild({
  id = 'measurement-1',
  name = 'temp-sensor-1',
  distance = 'atEquipment',
  positionVsParent = 'atEquipment',
  type = 'temperature',
 } = {}) {
  return {
    config: {
      general: { id, name },
      functionality: { distance, positionVsParent, softwareType: 'measurement' },
      asset: { type },
    },
    measurements: {
      emitter: new EventEmitter(),
    },
  };
 }
 module.exports = {
  makeUiConfig,
  makeReactorConfig,
  makeNodeStub,
  makeREDStub,
  makeMeasurementChild,
 };
--- a/test/integration/.gitkeep
+++ b/test/integration/.gitkeep
--- a/test/integration/measurement-temperature.integration.test.js
+++ b/test/integration/measurement-temperature.integration.test.js
@@ -0,0 +1,26 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR } = require('../../src/specificClass');
 const { makeReactorConfig, makeMeasurementChild } = require('../helpers/factories');
 test('measurement child temperature event updates reactor temperature', () => {
  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
  const measurement = makeMeasurementChild({
    type: 'temperature',
    distance: 'atEquipment',
    positionVsParent: 'upstream',
  });
  reactor.registerChild(measurement, 'measurement');
  measurement.measurements.emitter.emit('temperature.measured.atEquipment', {
    childName: 'T-1',
    value: 27.5,
    unit: 'C',
    timestamp: Date.now(),
  });
  assert.equal(reactor.temperature, 27.5);
 });
--- a/test/integration/otr-kla.integration.test.js
+++ b/test/integration/otr-kla.integration.test.js
@@ -0,0 +1,91 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 const NUM_SPECIES = 13;
 test('CSTR uses external OTR when kla is NaN', () => {
  const reactor = new Reactor_CSTR(
    makeReactorConfig({ reactor_type: 'CSTR', kla: NaN, n_inlets: 1 }),
  );
  reactor.asm = {
    compute_dC: () => Array(NUM_SPECIES).fill(0),
  };
  reactor.Fs[0] = 0;
  reactor.OTR = 4;
  reactor.state = Array(NUM_SPECIES).fill(0);
  reactor.tick(1);
  assert.equal(reactor.state[0], 4);
 });
 test('CSTR uses kla-based oxygen transfer when kla is finite', () => {
  const reactor = new Reactor_CSTR(
    makeReactorConfig({ reactor_type: 'CSTR', kla: 2, n_inlets: 1 }),
  );
  reactor.asm = {
    compute_dC: () => Array(NUM_SPECIES).fill(0),
  };
  reactor.Fs[0] = 0;
  reactor.OTR = 1;
  reactor.state = Array(NUM_SPECIES).fill(0);
  const expected = Math.min(
    reactor._calcOTR(0, reactor.temperature),
    reactor._calcOxygenSaturation(reactor.temperature),
  );
  reactor.tick(1);
  assert.ok(Math.abs(reactor.state[0] - expected) < 1e-9);
 });
 test('PFR uses external OTR branch when kla is NaN', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', kla: NaN, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
  );
  reactor.asm = {
    compute_dC: () => Array(NUM_SPECIES).fill(0),
  };
  reactor.Fs[0] = 0;
  reactor.D = 0;
  reactor.OTR = 3;
  reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
  reactor.tick(1);
  assert.equal(reactor.state[1][0], 4.5);
  assert.equal(reactor.state[2][0], 4.5);
  assert.equal(reactor.state[3][0], 4.5);
  assert.equal(reactor.state[4][0], 4.5);
 });
 test('PFR uses kla-based transfer branch when kla is finite', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', kla: 1, n_inlets: 1, length: 8, resolution_L: 6, volume: 40 }),
  );
  reactor.asm = {
    compute_dC: () => Array(NUM_SPECIES).fill(0),
  };
  reactor.Fs[0] = 0;
  reactor.D = 0;
  reactor.OTR = 0;
  reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
  const expected = Math.min(
    reactor._calcOTR(0, reactor.temperature) * (reactor.n_x / (reactor.n_x - 2)),
    reactor._calcOxygenSaturation(reactor.temperature),
  );
  reactor.tick(1);
  assert.ok(Math.abs(reactor.state[1][0] - expected) < 1e-9);
  assert.ok(Math.abs(reactor.state[2][0] - expected) < 1e-9);
  assert.ok(Math.abs(reactor.state[3][0] - expected) < 1e-9);
  assert.ok(Math.abs(reactor.state[4][0] - expected) < 1e-9);
 });
--- a/test/integration/pfr-boundary.integration.test.js
+++ b/test/integration/pfr-boundary.integration.test.js
@@ -0,0 +1,35 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_PFR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 test('_applyBoundaryConditions enforces Danckwerts inlet and Neumann outlet for flowing case', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50, alpha: 0.2 }),
  );
  reactor.Fs[0] = 2;
  reactor.Cs_in[0] = Array(13).fill(9);
  reactor.D = 1;
  const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i));
  reactor._applyBoundaryConditions(state);
  assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
  assert.equal(state[0].every((v) => Number.isFinite(v)), true);
 });
 test('_applyBoundaryConditions copies first interior slice when no flow is present', () => {
  const reactor = new Reactor_PFR(
    makeReactorConfig({ reactor_type: 'PFR', n_inlets: 1, length: 10, resolution_L: 5, volume: 50 }),
  );
  reactor.Fs[0] = 0;
  const state = Array.from({ length: reactor.n_x }, (_, i) => Array(13).fill(i + 10));
  reactor._applyBoundaryConditions(state);
  assert.deepEqual(state[0], state[1]);
  assert.deepEqual(state[reactor.n_x - 1], state[reactor.n_x - 2]);
 });
--- a/test/integration/structure-examples.integration.test.js
+++ b/test/integration/structure-examples.integration.test.js
@@ -0,0 +1,23 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('node:fs');
 const path = require('node:path');
 const dir = path.resolve(__dirname, '../../examples');
 function loadJson(file) {
  return JSON.parse(fs.readFileSync(path.join(dir, file), 'utf8'));
 }
 test('examples package exists for reactor', () => {
  for (const file of ['README.md', 'basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
    assert.equal(fs.existsSync(path.join(dir, file)), true, file + ' missing');
  }
 });
 test('example flows are parseable arrays for reactor', () => {
  for (const file of ['basic.flow.json', 'integration.flow.json', 'edge.flow.json']) {
    const parsed = loadJson(file);
    assert.equal(Array.isArray(parsed), true);
  }
 });
--- a/test/integration/tick-loop.integration.test.js
+++ b/test/integration/tick-loop.integration.test.js
@@ -0,0 +1,134 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const NodeClass = require('../../src/nodeClass');
 const { makeNodeStub } = require('../helpers/factories');
 test('_tick emits source effluent on process output', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  inst.node = node;
  inst._output = { formatMsg() { return null; } };
  inst.source = {
    get getEffluent() {
      return { topic: 'Fluent', payload: { inlet: 0, F: 1, C: [] }, timestamp: 1 };
    },
  };
  inst._tick();
  assert.equal(node._sent.length, 1);
  assert.equal(node._sent[0][0].topic, 'Fluent');
  assert.equal(node._sent[0][1], null);
  assert.equal(node._sent[0][2], null);
 });
 test('_tick emits reactor telemetry on influx output', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  let captured = null;
  inst.node = node;
  inst.config = { functionality: { softwareType: 'reactor' }, general: { id: 'reactor-node-1' } };
  inst._output = {
    formatMsg(output, config, format) {
      captured = { output, config, format };
      return { topic: 'reactor_reactor-node-1', payload: { measurement: 'reactor_reactor-node-1', fields: output } };
    }
  };
  inst.source = {
    temperature: 19.5,
    get getGridProfile() {
      return null;
    },
    get getEffluent() {
      return {
        topic: 'Fluent',
        payload: {
          inlet: 0,
          F: 42,
          C: [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500]
        },
        timestamp: 1
      };
    },
  };
  inst._tick();
  assert.equal(node._sent.length, 1);
  assert.equal(node._sent[0][0].topic, 'Fluent');
  assert.equal(node._sent[0][1].topic, 'reactor_reactor-node-1');
  assert.equal(captured.format, 'influxdb');
  assert.equal(captured.output.flow_total, 42);
  assert.equal(captured.output.temperature, 19.5);
  assert.equal(captured.output.S_O, 2.1);
  assert.equal(captured.output.S_NH, 16);
  assert.equal(captured.output.X_TS, 2500);
 });
 test('_startTickLoop schedules periodic tick after startup delay', () => {
  const inst = Object.create(NodeClass.prototype);
  const delays = [];
  const intervals = [];
  let tickCount = 0;
  inst._tick = () => {
    tickCount += 1;
  };
  const originalSetTimeout = global.setTimeout;
  const originalSetInterval = global.setInterval;
  global.setTimeout = (fn, ms) => {
    delays.push(ms);
    fn();
    return 10;
  };
  global.setInterval = (fn, ms) => {
    intervals.push(ms);
    fn();
    return 22;
  };
  try {
    inst._startTickLoop();
  } finally {
    global.setTimeout = originalSetTimeout;
    global.setInterval = originalSetInterval;
  }
  assert.deepEqual(delays, [1000]);
  assert.deepEqual(intervals, [1000]);
  assert.equal(inst._tickInterval, 22);
  assert.equal(tickCount, 1);
 });
 test('_attachCloseHandler clears tick interval and calls done callback', () => {
  const inst = Object.create(NodeClass.prototype);
  const node = makeNodeStub();
  inst.node = node;
  inst._tickInterval = 55;
  const cleared = [];
  const originalClearInterval = global.clearInterval;
  global.clearInterval = (id) => {
    cleared.push(id);
  };
  let doneCalled = 0;
  try {
    inst._attachCloseHandler();
    node._handlers.close(() => {
      doneCalled += 1;
    });
  } finally {
    global.clearInterval = originalClearInterval;
  }
  assert.deepEqual(cleared, [55]);
  assert.equal(doneCalled, 1);
 });
--- a/test/integration/upstream-reactor.integration.test.js
+++ b/test/integration/upstream-reactor.integration.test.js
@@ -0,0 +1,48 @@
 const test = require('node:test');
 const assert = require('node:assert/strict');
 const { Reactor_CSTR } = require('../../src/specificClass');
 const { makeReactorConfig } = require('../helpers/factories');
 const DAY_MS = 1000 * 60 * 60 * 24;
 test('registering upstream reactor subscribes to upstream stateChange events', () => {
  const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
  const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
  let calledWith = null;
  downstream.updateState = (timestamp) => {
    calledWith = timestamp;
  };
  downstream.registerChild(upstream, 'reactor');
  upstream.emitter.emit('stateChange', 12345);
  assert.equal(downstream.upstreamReactor, upstream);
  assert.equal(calledWith, 12345);
 });
 test('updateState pulls influent from upstream reactor effluent when linked', () => {
  const downstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1, timeStep: 1 }));
  const upstream = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1 }));
  upstream.Fs[0] = 3;
  upstream.state = Array(13).fill(11);
  downstream.upstreamReactor = upstream;
  downstream.currentTime = 0;
  downstream.timeStep = 1;
  downstream.speedUpFactor = 1;
  let ticks = 0;
  downstream.tick = () => {
    ticks += 1;
    return downstream.state;
  };
  downstream.updateState(DAY_MS);
  assert.equal(ticks, 1);
  assert.equal(downstream.Fs[0], 3);
  assert.deepEqual(downstream.Cs_in[0], Array(13).fill(11));
 });
--- a/test/specificClass.test.js
+++ b/test/specificClass.test.js
@@ -0,0 +1,346 @@
 /**
 * Tests for reactor specificClass (domain logic).
 *
 * Two reactor classes are exported: Reactor_CSTR and Reactor_PFR.
 * Both extend a base Reactor class.
 *
 * Key methods tested:
 *  - _calcOTR: oxygen transfer rate calculation
 *  - _arrayClip2Zero: clip negative values to zero
 *  - setInfluent / getEffluent: influent/effluent data flow
 *  - setOTR: external OTR override
 *  - tick (CSTR): forward Euler state update
 *  - tick (PFR): finite difference state update
 *  - registerChild: dispatches to measurement / reactor handlers
 */
 const { Reactor_CSTR, Reactor_PFR } = require('../src/specificClass');
 // --------------- helpers ---------------
 const NUM_SPECIES = 13;
 function makeCSTRConfig(overrides = {}) {
  return {
    general: {
      name: 'TestCSTR',
      id: 'cstr-test-1',
      logging: { enabled: false, logLevel: 'error' },
    },
    functionality: {
      softwareType: 'reactor',
      positionVsParent: 'atEquipment',
    },
    volume: 1000,
    n_inlets: 1,
    kla: 240,
    timeStep: 1,      // 1 second
    initialState: new Array(NUM_SPECIES).fill(1.0),
    ...overrides,
  };
 }
 function makePFRConfig(overrides = {}) {
  return {
    general: {
      name: 'TestPFR',
      id: 'pfr-test-1',
      logging: { enabled: false, logLevel: 'error' },
    },
    functionality: {
      softwareType: 'reactor',
      positionVsParent: 'atEquipment',
    },
    volume: 200,
    length: 10,
    resolution_L: 10,
    n_inlets: 1,
    kla: 240,
    alpha: 0.5,
    timeStep: 1,
    initialState: new Array(NUM_SPECIES).fill(0.1),
    ...overrides,
  };
 }
 // --------------- CSTR tests ---------------
 describe('Reactor_CSTR', () => {
  describe('constructor / initialization', () => {
    it('should create an instance and set state from initialState', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      expect(r).toBeDefined();
      expect(r.state).toEqual(new Array(NUM_SPECIES).fill(1.0));
    });
    it('should initialize Fs and Cs_in arrays based on n_inlets', () => {
      const r = new Reactor_CSTR(makeCSTRConfig({ n_inlets: 3 }));
      expect(r.Fs).toHaveLength(3);
      expect(r.Cs_in).toHaveLength(3);
      expect(r.Fs.every(v => v === 0)).toBe(true);
    });
    it('should store volume from config', () => {
      const r = new Reactor_CSTR(makeCSTRConfig({ volume: 500 }));
      expect(r.volume).toBe(500);
    });
    it('should initialize temperature to 20', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      expect(r.temperature).toBe(20);
    });
  });
  describe('_calcOTR()', () => {
    let r;
    beforeAll(() => { r = new Reactor_CSTR(makeCSTRConfig({ kla: 240 })); });
    it('should return a positive value when S_O < saturation', () => {
      const otr = r._calcOTR(0, 20);
      expect(otr).toBeGreaterThan(0);
    });
    it('should return approximately zero when S_O equals saturation', () => {
      // S_O_sat at T=20: 14.652 - 4.1022e-1*20 + 7.9910e-3*400 + 7.7774e-5*8000
      const T = 20;
      const S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T * T + 7.7774e-5 * T * T * T;
      const otr = r._calcOTR(S_O_sat, T);
      expect(otr).toBeCloseTo(0, 5);
    });
    it('should return a negative value when S_O > saturation (supersaturated)', () => {
      const otr = r._calcOTR(100, 20);
      expect(otr).toBeLessThan(0);
    });
    it('should use T=20 as default temperature', () => {
      const otr1 = r._calcOTR(0);
      const otr2 = r._calcOTR(0, 20);
      expect(otr1).toBe(otr2);
    });
  });
  describe('_arrayClip2Zero()', () => {
    let r;
    beforeAll(() => { r = new Reactor_CSTR(makeCSTRConfig()); });
    it('should clip negative values to zero', () => {
      expect(r._arrayClip2Zero([-5, 3, -1, 0, 7])).toEqual([0, 3, 0, 0, 7]);
    });
    it('should leave all-positive arrays unchanged', () => {
      expect(r._arrayClip2Zero([1, 2, 3])).toEqual([1, 2, 3]);
    });
    it('should handle nested arrays (2D)', () => {
      const result = r._arrayClip2Zero([[-1, 2], [3, -4]]);
      expect(result).toEqual([[0, 2], [3, 0]]);
    });
    it('should handle a single scalar', () => {
      expect(r._arrayClip2Zero(-5)).toBe(0);
      expect(r._arrayClip2Zero(5)).toBe(5);
    });
  });
  describe('setInfluent / getEffluent', () => {
    it('should store influent data via setter', () => {
      const r = new Reactor_CSTR(makeCSTRConfig({ n_inlets: 2 }));
      const input = {
        payload: {
          inlet: 0,
          F: 100,
          C: new Array(NUM_SPECIES).fill(5),
        },
      };
      r.setInfluent = input;
      expect(r.Fs[0]).toBe(100);
      expect(r.Cs_in[0]).toEqual(new Array(NUM_SPECIES).fill(5));
    });
    it('should return effluent with the sum of Fs and the current state', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      r.Fs[0] = 50;
      const eff = r.getEffluent;
      expect(eff.topic).toBe('Fluent');
      expect(eff.payload.F).toBe(50);
      expect(eff.payload.C).toEqual(r.state);
    });
  });
  describe('setOTR', () => {
    it('should set the OTR value', () => {
      const r = new Reactor_CSTR(makeCSTRConfig({ kla: NaN }));
      r.setOTR = { payload: 42 };
      expect(r.OTR).toBe(42);
    });
  });
  describe('tick()', () => {
    it('should return a new state array of correct length', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      const result = r.tick(0.001);
      expect(result).toHaveLength(NUM_SPECIES);
    });
    it('should not produce NaN values', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      r.Fs[0] = 10;
      r.Cs_in[0] = new Array(NUM_SPECIES).fill(5);
      const result = r.tick(0.001);
      result.forEach(v => expect(Number.isNaN(v)).toBe(false));
    });
    it('should not produce negative concentrations', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      // Run multiple ticks
      for (let i = 0; i < 100; i++) {
        r.tick(0.001);
      }
      r.state.forEach(v => expect(v).toBeGreaterThanOrEqual(0));
    });
    it('should reach steady state with zero flow (concentrations change only via reaction)', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      // No inflow
      const initial = [...r.state];
      r.tick(0.0001);
      // State should have changed due to reaction/OTR
      const changed = r.state.some((v, i) => v !== initial[i]);
      expect(changed).toBe(true);
    });
  });
  describe('registerChild()', () => {
    it('should not throw for "measurement" software type', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      // Passing null child will trigger warn but not crash
      expect(() => r.registerChild(null, 'measurement')).not.toThrow();
    });
    it('should not throw for "reactor" software type', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      expect(() => r.registerChild(null, 'reactor')).not.toThrow();
    });
    it('should not throw for unknown software type', () => {
      const r = new Reactor_CSTR(makeCSTRConfig());
      expect(() => r.registerChild(null, 'unknown')).not.toThrow();
    });
  });
 });
 // --------------- PFR tests ---------------
 describe('Reactor_PFR', () => {
  describe('constructor / initialization', () => {
    it('should create an instance with 2D state grid', () => {
      const r = new Reactor_PFR(makePFRConfig());
      expect(r).toBeDefined();
      expect(r.state).toHaveLength(10); // resolution_L = 10
      expect(r.state[0]).toHaveLength(NUM_SPECIES);
    });
    it('should compute d_x = length / n_x', () => {
      const r = new Reactor_PFR(makePFRConfig({ length: 10, resolution_L: 5 }));
      expect(r.d_x).toBe(2);
    });
    it('should compute cross-sectional area A = volume / length', () => {
      const r = new Reactor_PFR(makePFRConfig({ volume: 200, length: 10 }));
      expect(r.A).toBe(20);
    });
    it('should initialize D (dispersion) to 0', () => {
      const r = new Reactor_PFR(makePFRConfig());
      expect(r.D).toBe(0);
    });
    it('should create derivative operators of correct size', () => {
      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 8 }));
      expect(r.D_op).toHaveLength(8);
      expect(r.D_op[0]).toHaveLength(8);
      expect(r.D2_op).toHaveLength(8);
      expect(r.D2_op[0]).toHaveLength(8);
    });
  });
  describe('setDispersion', () => {
    it('should set the axial dispersion value', () => {
      const r = new Reactor_PFR(makePFRConfig());
      r.setDispersion = { payload: 0.5 };
      expect(r.D).toBe(0.5);
    });
  });
  describe('tick()', () => {
    it('should return a 2D state grid of correct dimensions', () => {
      const r = new Reactor_PFR(makePFRConfig());
      r.D = 0.01;
      const result = r.tick(0.0001);
      expect(result).toHaveLength(10);
      expect(result[0]).toHaveLength(NUM_SPECIES);
    });
    it('should not produce NaN values with small time step and dispersion', () => {
      const r = new Reactor_PFR(makePFRConfig());
      r.D = 0.01;
      r.Fs[0] = 10;
      r.Cs_in[0] = new Array(NUM_SPECIES).fill(5);
      const result = r.tick(0.0001);
      result.forEach(row => {
        row.forEach(v => expect(Number.isNaN(v)).toBe(false));
      });
    });
    it('should not produce negative concentrations', () => {
      const r = new Reactor_PFR(makePFRConfig());
      r.D = 0.01;
      for (let i = 0; i < 10; i++) {
        r.tick(0.0001);
      }
      r.state.forEach(row => {
        row.forEach(v => expect(v).toBeGreaterThanOrEqual(0));
      });
    });
  });
  describe('_applyBoundaryConditions()', () => {
    it('should apply Neumann BC at outlet (last = second to last)', () => {
      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 5 }));
      const state = Array.from({ length: 5 }, () => new Array(NUM_SPECIES).fill(1));
      state[3] = new Array(NUM_SPECIES).fill(7);
      r._applyBoundaryConditions(state);
      // outlet BC: state[4] = state[3]
      expect(state[4]).toEqual(new Array(NUM_SPECIES).fill(7));
    });
    it('should apply Neumann BC at inlet when no flow', () => {
      const r = new Reactor_PFR(makePFRConfig({ resolution_L: 5 }));
      r.Fs[0] = 0;
      const state = Array.from({ length: 5 }, () => new Array(NUM_SPECIES).fill(1));
      state[1] = new Array(NUM_SPECIES).fill(3);
      r._applyBoundaryConditions(state);
      // No flow: state[0] = state[1]
      expect(state[0]).toEqual(new Array(NUM_SPECIES).fill(3));
    });
  });
  describe('_arrayClip2Zero() (inherited)', () => {
    it('should clip 2D arrays correctly', () => {
      const r = new Reactor_PFR(makePFRConfig());
      const result = r._arrayClip2Zero([[-1, 2], [3, -4]]);
      expect(result).toEqual([[0, 2], [3, 0]]);
    });
  });
  describe('_calcOTR() (inherited)', () => {
    it('should work the same as in CSTR', () => {
      const r = new Reactor_PFR(makePFRConfig({ kla: 240 }));
      const otr = r._calcOTR(0, 20);
      expect(otr).toBeGreaterThan(0);
    });
  });
 });
Author	SHA1	Message	Date
znetsixe	c5fc5c1b59	docs: add CLAUDE.md with S88 classification and superproject rule reference References the flow-layout rule set in the EVOLV superproject (.claude/rules/node-red-flow-layout.md) so Claude Code sessions working in this repo know the S88 level, colour, and placement lane for this node. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>	2026-04-14 07:47:25 +02:00
znetsixe	556dc39049	Merge remote-tracking branch 'origin/main' into dev-Rene # Conflicts: # additional_nodes/recirculation-pump.js # additional_nodes/settling-basin.js # reactor.html # src/nodeClass.js # src/reaction_modules/asm3_class Koch.js # src/reaction_modules/asm3_class.js # src/specificClass.js	2026-03-31 16:20:45 +02:00
root	2e3ba8a9bf	Expand reactor demo telemetry and stability handling	2026-03-31 14:26:10 +02:00
Rene De Ren	1da55fc3f5	Expose output format selectors in editor	2026-03-12 16:39:25 +01:00
Rene De Ren	06251988af	fix: replace console usage with logger, throw on unknown reactor type Unknown reactor type is a configuration error that should fail loudly. Converted console.log to logger.warn for unknown topics. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-12 09:33:34 +01:00
Rene De Ren	7ff7c6ec1d	test: add unit tests for specificClass Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>	2026-03-11 16:31:53 +01:00
znetsixe	2c69a5a0c1	updates	2026-03-11 11:13:51 +01:00
znetsixe	460b872053	updates	2026-02-23 12:51:10 +01:00
znetsixe	2b9ad5fd19	before functional changes by codex	2026-02-19 17:37:42 +01:00
znetsixe	7c8722b324	changed colours and icon based on s88	2025-10-14 13:52:55 +02:00