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>

.gitignore

@@ -1,136 +1,136 @@
-# Logs
+# Logs
-logs
+logs
-*.log
+*.log
-npm-debug.log*
+npm-debug.log*
-yarn-debug.log*
+yarn-debug.log*
-yarn-error.log*
+yarn-error.log*
-lerna-debug.log*
+lerna-debug.log*
-.pnpm-debug.log*
+.pnpm-debug.log*
-
+
-# Diagnostic reports (https://nodejs.org/api/report.html)
+# Diagnostic reports (https://nodejs.org/api/report.html)
-report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
-
+
-# Runtime data
+# Runtime data
-pids
+pids
-*.pid
+*.pid
-*.seed
+*.seed
-*.pid.lock
+*.pid.lock
-
+
-# Directory for instrumented libs generated by jscoverage/JSCover
+# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
+lib-cov
-
+
-# Coverage directory used by tools like istanbul
+# Coverage directory used by tools like istanbul
-coverage
+coverage
-*.lcov
+*.lcov
-
+
-# nyc test coverage
+# nyc test coverage
-.nyc_output
+.nyc_output
-
+
-# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
+.grunt
-
+
-# Bower dependency directory (https://bower.io/)
+# Bower dependency directory (https://bower.io/)
-bower_components
+bower_components
-
+
-# node-waf configuration
+# node-waf configuration
-.lock-wscript
+.lock-wscript
-
+
-# Compiled binary addons (https://nodejs.org/api/addons.html)
+# Compiled binary addons (https://nodejs.org/api/addons.html)
-build/Release
+build/Release
-
+
-# Dependency directories
+# Dependency directories
-node_modules/
+node_modules/
-jspm_packages/
+jspm_packages/
-
+
-# Snowpack dependency directory (https://snowpack.dev/)
+# Snowpack dependency directory (https://snowpack.dev/)
-web_modules/
+web_modules/
-
+
-# TypeScript cache
+# TypeScript cache
-*.tsbuildinfo
+*.tsbuildinfo
-
+
-# Optional npm cache directory
+# Optional npm cache directory
-.npm
+.npm
-
+
-# Optional eslint cache
+# Optional eslint cache
-.eslintcache
+.eslintcache
-
+
-# Optional stylelint cache
+# Optional stylelint cache
-.stylelintcache
+.stylelintcache
-
+
-# Microbundle cache
+# Microbundle cache
-.rpt2_cache/
+.rpt2_cache/
-.rts2_cache_cjs/
+.rts2_cache_cjs/
-.rts2_cache_es/
+.rts2_cache_es/
-.rts2_cache_umd/
+.rts2_cache_umd/
-
+
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+# Optional REPL history
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+# Output of 'npm pack'
-*.tgz
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-# Yarn Integrity file
+# Yarn Integrity file
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+.yarn-integrity
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+# dotenv environment variable files
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+.env
-.env.development.local
+.env.development.local
-.env.test.local
+.env.test.local
-.env.production.local
+.env.production.local
-.env.local
+.env.local
-
+
-# parcel-bundler cache (https://parceljs.org/)
+# parcel-bundler cache (https://parceljs.org/)
-.cache
+.cache
-.parcel-cache
+.parcel-cache
-
+
-# Next.js build output
+# Next.js build output
-.next
+.next
-out
+out
-
+
-# Nuxt.js build / generate output
+# Nuxt.js build / generate output
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+.nuxt
-dist
+dist
-
+
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+.cache/
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+# Comment in the public line in if your project uses Gatsby and not Next.js
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+# https://nextjs.org/blog/next-9-1#public-directory-support
-# public
+# public
-
+
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+# vuepress build output
-.vuepress/dist
+.vuepress/dist
-
+
-# vuepress v2.x temp and cache directory
+# vuepress v2.x temp and cache directory
-.temp
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+
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+# Stores VSCode versions used for testing VSCode extensions
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+.vscode-test
-
+
-# yarn v2
+# yarn v2
-.yarn/cache
+.yarn/cache
-.yarn/unplugged
+.yarn/unplugged
-.yarn/build-state.yml
+.yarn/build-state.yml
-.yarn/install-state.gz
+.yarn/install-state.gz
-.pnp.*
+.pnp.*

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).

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-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.

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.
-
+

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>

additional_nodes/recirculation-pump.js

@@ -3,13 +3,12 @@ module.exports = function(RED) {
         RED.nodes.createNode(this, config);
         var node = this;
 
-        let name = config.name;
         let F2 = parseFloat(config.F2);
         const inlet_F2 = parseInt(config.inlet);
 
         node.on('input', function(msg, send, done) {
             switch (msg.topic) {
-                case "Fluent":
+                case "Fluent": {
                     // conserve volume flow debit
                     let F_in = msg.payload.F;
                     let F1 = Math.max(F_in - F2, 0);
@@ -24,6 +23,7 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
+                }
                 case "clock":
                     break;
                 default:

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>

additional_nodes/settling-basin.js

@@ -3,13 +3,12 @@ module.exports = function(RED) {
         RED.nodes.createNode(this, config);
         var node = this;
 
-        let name = config.name;
         let TS_set = parseFloat(config.TS_set);
         const inlet_sludge = parseInt(config.inlet);
 
         node.on('input', function(msg, send, done) {
             switch (msg.topic) {
-                case "Fluent":
+                case "Fluent": {
                     // conserve volume flow debit
                     let F_in = msg.payload.F;
                     let C_in = msg.payload.C;
@@ -41,6 +40,7 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
+                }
                 case "clock":
                     break;
                 default:

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"
-      }
+      }
-    }
+    }
-  }
+  }
-}
+}

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 --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"
-  }
+  }
-}
+}

reactor.html

@@ -23,7 +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 },
@@ -40,6 +40,8 @@
 
             timeStep: { value: 1, required: true },
             speedUpFactor: { value: 1 },
+            processOutputFormat: { value: "process" },
+            dbaseOutputFormat: { value: "influxdb" },
 
             enableLog: { value: false },
             logLevel: { value: "error" },
@@ -252,6 +254,23 @@
         <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>

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}`);
-        }
+        }
-    });
+    });
-};
+};

src/nodeClass.js

@@ -1,4 +1,21 @@
 const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
+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 {
@@ -18,6 +35,7 @@ class nodeClass {
 
         this._loadConfig(uiConfig)
         this._setupClass();
+        this._output = new outputUtils();
 
         this._attachInputHandler();
         this._registerChild();
@@ -72,24 +90,14 @@ class nodeClass {
     }
 
     /**
-     * Parse node configuration
+     * Parse node configuration using ConfigManager
      * @param {object} uiConfig Config set in UI in node-red
      */
     _loadConfig(uiConfig) {
-        this.config = {
+        const cfgMgr = new configManager();
-            general: {
+
-                name: uiConfig.name || this.name,
+        // Build config: base sections + reactor-specific domain config
-                id: this.node.id,
+        this.config = cfgMgr.buildConfig('reactor', uiConfig, this.node.id, {
-                unit: null,
-                logging: {
-                    enabled: uiConfig.enableLog,
-                    logLevel: uiConfig.logLevel
-                }
-            },
-            functionality: {
-                positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
-                softwareType: "reactor" // should be set in config manager
-            },
             reactor_type: uiConfig.reactor_type,
             volume: parseFloat(uiConfig.volume),
             length: parseFloat(uiConfig.length),
@@ -114,7 +122,7 @@ class nodeClass {
             ],
             timeStep: parseFloat(uiConfig.timeStep),
             speedUpFactor: Number(uiConfig.speedUpFactor) || 1
-        }
+        });
     }
 
     /**
@@ -164,7 +172,29 @@ class nodeClass {
         if (gridProfile) {
             this.node.send([{ topic: "GridProfile", payload: gridProfile }, null, null]);
         }
-        this.node.send([this.source.getEffluent, 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() {

src/reaction_modules/asm3_class Koch.js

@@ -13,7 +13,7 @@ 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        [-]
@@ -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) {
@@ -171,7 +171,7 @@ class ASM3 {
   compute_rates(state, T = 20) {
     // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
     const rates = Array(12);
-    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
+    const [S_O, , S_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 
@@ -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;

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) {
@@ -171,7 +171,7 @@ class ASM3 {
   compute_rates(state, T = 20) {
     // state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
     const rates = Array(12);
-    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
+    const [S_O, , S_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 
@@ -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;

src/specificClass.js

@@ -1,7 +1,7 @@
 const ASM3 = require('./reaction_modules/asm3_class.js');
 const { create, all, isArray } = require('mathjs');
 const { assertNoNaN } = require('./utils.js');
-const { childRegistrationUtils, logger, MeasurementContainer } = require('generalFunctions');
+const { childRegistrationUtils, logger, MeasurementContainer, POSITIONS } = require('generalFunctions');
 const EventEmitter = require('events');
 
 const mathConfig = {
@@ -104,6 +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.
@@ -146,7 +169,6 @@ class Reactor {
       position = measurement.config.functionality.positionVsParent;
     }
     const measurementType = measurement.config.asset.type;
-    const key = `${measurementType}_${position}`;
     const eventName = `${measurementType}.measured.${position}`;
 
     // Register event listener for measurement updates
@@ -159,7 +181,7 @@ class Reactor {
         .variant("measured")
         .position(position)
         .value(eventData.value, eventData.timestamp, eventData.unit);
-      
+
       this._updateMeasurement(measurementType, eventData.value, position, eventData);
     });
   }
@@ -179,12 +201,12 @@ class Reactor {
     });
   }
 
-  
+
-  _updateMeasurement(measurementType, value, position, context) {
+  _updateMeasurement(measurementType, value, position, _context) {
     this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
     switch (measurementType) {
       case "temperature":
-        if (position == "atEquipment") {
+        if (position == POSITIONS.AT_EQUIPMENT) {
           this.temperature = value;
         }
         break;
@@ -241,7 +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");
@@ -302,7 +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) {
@@ -348,7 +370,7 @@ 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;
   }
 

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 };

test/basic/grid-profile.basic.test.js

@@ -1,45 +1,45 @@
-const test = require('node:test');
+const test = require('node:test');
-const assert = require('node:assert/strict');
+const assert = require('node:assert/strict');
-
+
-const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
+const { Reactor_CSTR, Reactor_PFR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
+const { makeReactorConfig } = require('../helpers/factories');
-
+
-test('CSTR getGridProfile returns null', () => {
+test('CSTR getGridProfile returns null', () => {
-  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
+  const reactor = new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR' }));
-  assert.equal(reactor.getGridProfile, null);
+  assert.equal(reactor.getGridProfile, null);
-});
+});
-
+
-test('PFR getGridProfile returns state matrix with correct dimensions', () => {
+test('PFR getGridProfile returns state matrix with correct dimensions', () => {
-  const n_x = 8;
+  const n_x = 8;
-  const length = 40;
+  const length = 40;
-  const reactor = new Reactor_PFR(
+  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', resolution_L: n_x, length }),
+    makeReactorConfig({ reactor_type: 'PFR', resolution_L: n_x, length }),
-  );
+  );
-
+
-  const profile = reactor.getGridProfile;
+  const profile = reactor.getGridProfile;
-  assert.notEqual(profile, null);
+  assert.notEqual(profile, null);
-  assert.equal(profile.n_x, n_x);
+  assert.equal(profile.n_x, n_x);
-  assert.equal(profile.d_x, length / n_x);
+  assert.equal(profile.d_x, length / n_x);
-  assert.equal(profile.length, length);
+  assert.equal(profile.length, length);
-  assert.equal(profile.grid.length, n_x, 'grid should have n_x rows');
+  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.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.ok(Array.isArray(profile.species), 'species list should be an array');
-  assert.equal(profile.species.length, 13);
+  assert.equal(profile.species.length, 13);
-  assert.equal(profile.species[3], 'S_NH');
+  assert.equal(profile.species[3], 'S_NH');
-  assert.equal(typeof profile.timestamp, 'number');
+  assert.equal(typeof profile.timestamp, 'number');
-});
+});
-
+
-test('PFR getGridProfile is mutation-safe', () => {
+test('PFR getGridProfile is mutation-safe', () => {
-  const reactor = new Reactor_PFR(
+  const reactor = new Reactor_PFR(
-    makeReactorConfig({ reactor_type: 'PFR', resolution_L: 5, length: 10 }),
+    makeReactorConfig({ reactor_type: 'PFR', resolution_L: 5, length: 10 }),
-  );
+  );
-
+
-  const profile = reactor.getGridProfile;
+  const profile = reactor.getGridProfile;
-  const originalValue = reactor.state[0][3]; // S_NH at cell 0
+  const originalValue = reactor.state[0][3]; // S_NH at cell 0
-
+
-  // Mutate the returned grid
+  // Mutate the returned grid
-  profile.grid[0][3] = 999;
+  profile.grid[0][3] = 999;
-
+
-  // Reactor internal state should be unchanged
+  // Reactor internal state should be unchanged
-  assert.equal(reactor.state[0][3], originalValue, 'mutating grid copy must not affect reactor state');
+  assert.equal(reactor.state[0][3], originalValue, 'mutating grid copy must not affect reactor state');
-});
+});

test/basic/speedup-factor.basic.test.js

@@ -1,68 +1,68 @@
-const test = require('node:test');
+const test = require('node:test');
-const assert = require('node:assert/strict');
+const assert = require('node:assert/strict');
-
+
-const { Reactor_CSTR } = require('../../src/specificClass');
+const { Reactor_CSTR } = require('../../src/specificClass');
-const nodeClass = require('../../src/nodeClass');
+const nodeClass = require('../../src/nodeClass');
-const { makeReactorConfig, makeUiConfig, makeNodeStub, makeREDStub } = require('../helpers/factories');
+const { makeReactorConfig, makeUiConfig, makeNodeStub, makeREDStub } = require('../helpers/factories');
-
+
-/**
+/**
- * Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
+ * Smoke tests for Fix 3: configurable speedUpFactor on Reactor.
- */
+ */
-
+
-test('specificClass defaults speedUpFactor to 1 when not in config', () => {
+test('specificClass defaults speedUpFactor to 1 when not in config', () => {
-  const config = makeReactorConfig();
+  const config = makeReactorConfig();
-  const reactor = new Reactor_CSTR(config);
+  const reactor = new Reactor_CSTR(config);
-  assert.equal(reactor.speedUpFactor, 1, 'speedUpFactor should default to 1');
+  assert.equal(reactor.speedUpFactor, 1, 'speedUpFactor should default to 1');
-});
+});
-
+
-test('specificClass accepts speedUpFactor from config', () => {
+test('specificClass accepts speedUpFactor from config', () => {
-  const config = makeReactorConfig();
+  const config = makeReactorConfig();
-  config.speedUpFactor = 10;
+  config.speedUpFactor = 10;
-  const reactor = new Reactor_CSTR(config);
+  const reactor = new Reactor_CSTR(config);
-  assert.equal(reactor.speedUpFactor, 10, 'speedUpFactor should be read from config');
+  assert.equal(reactor.speedUpFactor, 10, 'speedUpFactor should be read from config');
-});
+});
-
+
-test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () => {
+test('specificClass accepts speedUpFactor = 60 for accelerated simulation', () => {
-  const config = makeReactorConfig();
+  const config = makeReactorConfig();
-  config.speedUpFactor = 60;
+  config.speedUpFactor = 60;
-  const reactor = new Reactor_CSTR(config);
+  const reactor = new Reactor_CSTR(config);
-  assert.equal(reactor.speedUpFactor, 60, 'speedUpFactor=60 should be accepted');
+  assert.equal(reactor.speedUpFactor, 60, 'speedUpFactor=60 should be accepted');
-});
+});
-
+
-test('nodeClass passes speedUpFactor from uiConfig to reactor config', () => {
+test('nodeClass passes speedUpFactor from uiConfig to reactor config', () => {
-  const uiConfig = makeUiConfig({ speedUpFactor: 5 });
+  const uiConfig = makeUiConfig({ speedUpFactor: 5 });
-  const node = makeNodeStub();
+  const node = makeNodeStub();
-  const RED = makeREDStub();
+  const RED = makeREDStub();
-
+
-  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
+  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
-  assert.equal(nc.source.speedUpFactor, 5, 'nodeClass should pass speedUpFactor=5 to specificClass');
+  assert.equal(nc.source.speedUpFactor, 5, 'nodeClass should pass speedUpFactor=5 to specificClass');
-});
+});
-
+
-test('nodeClass defaults speedUpFactor to 1 when not in uiConfig', () => {
+test('nodeClass defaults speedUpFactor to 1 when not in uiConfig', () => {
-  const uiConfig = makeUiConfig();
+  const uiConfig = makeUiConfig();
-  // Ensure speedUpFactor is not set
+  // Ensure speedUpFactor is not set
-  delete uiConfig.speedUpFactor;
+  delete uiConfig.speedUpFactor;
-
+
-  const node = makeNodeStub();
+  const node = makeNodeStub();
-  const RED = makeREDStub();
+  const RED = makeREDStub();
-
+
-  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
+  const nc = new nodeClass(uiConfig, RED, node, 'test-reactor');
-  assert.equal(nc.source.speedUpFactor, 1, 'nodeClass should default speedUpFactor to 1');
+  assert.equal(nc.source.speedUpFactor, 1, 'nodeClass should default speedUpFactor to 1');
-});
+});
-
+
-test('updateState with speedUpFactor=1 advances roughly real-time', () => {
+test('updateState with speedUpFactor=1 advances roughly real-time', () => {
-  const config = makeReactorConfig();
+  const config = makeReactorConfig();
-  config.speedUpFactor = 1;
+  config.speedUpFactor = 1;
-  config.n_inlets = 1;
+  config.n_inlets = 1;
-  const reactor = new Reactor_CSTR(config);
+  const reactor = new Reactor_CSTR(config);
-
+
-  // Set a known start time
+  // Set a known start time
-  const t0 = reactor.currentTime;
+  const t0 = reactor.currentTime;
-  // Advance by 2 seconds real time
+  // Advance by 2 seconds real time
-  reactor.updateState(t0 + 2000);
+  reactor.updateState(t0 + 2000);
-
+
-  // With speedUpFactor=1, simulation should have advanced ~2 seconds worth
+  // With speedUpFactor=1, simulation should have advanced ~2 seconds worth
-  // (not 120 seconds like with the old hardcoded 60x factor)
+  // (not 120 seconds like with the old hardcoded 60x factor)
-  const elapsed = reactor.currentTime - t0;
+  const elapsed = reactor.currentTime - t0;
-  assert.ok(elapsed < 5000, `Elapsed ${elapsed}ms should be close to 2000ms, not 120000ms (old 60x factor)`);
+  assert.ok(elapsed < 5000, `Elapsed ${elapsed}ms should be close to 2000ms, not 120000ms (old 60x factor)`);
-});
+});

test/integration/otr-kla.integration.test.js

@@ -35,7 +35,10 @@ test('CSTR uses kla-based oxygen transfer when kla is finite', () => {
   reactor.OTR = 1;
   reactor.state = Array(NUM_SPECIES).fill(0);
 
-  const expected = reactor._calcOTR(0, reactor.temperature);
+  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);
@@ -75,7 +78,10 @@ test('PFR uses kla-based transfer branch when kla is finite', () => {
   reactor.OTR = 0;
   reactor.state = Array.from({ length: reactor.n_x }, () => Array(NUM_SPECIES).fill(0));
 
-  const expected = reactor._calcOTR(0, reactor.temperature) * (reactor.n_x / (reactor.n_x - 2));
+  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);

test/integration/tick-loop.integration.test.js

@@ -9,6 +9,7 @@ test('_tick emits source effluent on process output', () => {
   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 };
@@ -23,6 +24,50 @@ test('_tick emits source effluent on process output', () => {
   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 = [];

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);
+    });
+  });
+});