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

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).

LICENSE

@@ -1,190 +1,190 @@
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+use is covered by a right of the copyright holder of the Work).
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+In this Licence, the following terms have the following meaning:
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+— ‘The Original Work’:the work or software distributed or communicated by the Licensor under this Licence, available
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+exclusive rights of the rights owners in the Work, of the exhaustion of those rights or of other applicable limitations
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+The grant of the rights mentioned above is subject to some restrictions and obligations imposed on the Licensee. Those
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+Attribution right: The Licensee shall keep intact all copyright, patent or trademarks notices and all notices that refer to
+the Licence and to the disclaimer of warranties. The Licensee must include a copy of such notices and a copy of the
+Licence with every copy of the Work he/she distributes or communicates. The Licensee must cause any Derivative Work
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+
+Copyleft clause: If the Licensee distributes or communicates copies of the Original Works or Derivative Works, this
+Distribution or Communication will be done under the terms of this Licence or of a later version of this Licence unless
+the Original Work is expressly distributed only under this version of the Licence — for example by communicating
+‘EUPL v. 1.2 only’. The Licensee (becoming Licensor) cannot offer or impose any additional terms or conditions on the
+Work or Derivative Work that alter or restrict the terms of the Licence.
+
+Compatibility clause: If the Licensee Distributes or Communicates Derivative Works or copies thereof based upon both
+the Work and another work licensed under a Compatible Licence, this Distribution or Communication can be done
+under the terms of this Compatible Licence. For the sake of this clause, ‘Compatible Licence’ refers to the licences listed
+in the appendix attached to this Licence. Should the Licensee's obligations under the Compatible Licence conflict with
+his/her obligations under this Licence, the obligations of the Compatible Licence shall prevail.
+
+Provision of Source Code: When distributing or communicating copies of the Work, the Licensee will provide
+a machine-readable copy of the Source Code or indicate a repository where this Source will be easily and freely available
+for as long as the Licensee continues to distribute or communicate the Work.
+Legal Protection: This Licence does not grant permission to use the trade names, trademarks, service marks, or names
+of the Licensor, except as required for reasonable and customary use in describing the origin of the Work and
+reproducing the content of the copyright notice.
+
+6.Chain of Authorship
+The original Licensor warrants that the copyright in the Original Work granted hereunder is owned by him/her or
+licensed to him/her and that he/she has the power and authority to grant the Licence.
+Each Contributor warrants that the copyright in the modifications he/she brings to the Work are owned by him/her or
+licensed to him/her and that he/she has the power and authority to grant the Licence.
+Each time You accept the Licence, the original Licensor and subsequent Contributors grant You a licence to their contributions
+to the Work, under the terms of this Licence.
+
+7.Disclaimer of Warranty
+The Work is a work in progress, which is continuously improved by numerous Contributors. It is not a finished work
+and may therefore contain defects or ‘bugs’ inherent to this type of development.
+For the above reason, the Work is provided under the Licence on an ‘as is’ basis and without warranties of any kind
+concerning the Work, including without limitation merchantability, fitness for a particular purpose, absence of defects or
+errors, accuracy, non-infringement of intellectual property rights other than copyright as stated in Article 6 of this
+Licence.
+This disclaimer of warranty is an essential part of the Licence and a condition for the grant of any rights to the Work.
+
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+Except in the cases of wilful misconduct or damages directly caused to natural persons, the Licensor will in no event be
+liable for any direct or indirect, material or moral, damages of any kind, arising out of the Licence or of the use of the
+Work, including without limitation, damages for loss of goodwill, work stoppage, computer failure or malfunction, loss
+of data or any commercial damage, even if the Licensor has been advised of the possibility of such damage. However,
+the Licensor will be liable under statutory product liability laws as far such laws apply to the Work.
+
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+While distributing the Work, You may choose to conclude an additional agreement, defining obligations or services
+consistent with this Licence. However, if accepting obligations, You may act only on your own behalf and on your sole
+responsibility, not on behalf of the original Licensor or any other Contributor, and only if You agree to indemnify,
+defend, and hold each Contributor harmless for any liability incurred by, or claims asserted against such Contributor by
+the fact You have accepted any warranty or additional liability.
+
+10.Acceptance of the Licence
+The provisions of this Licence can be accepted by clicking on an icon ‘I agree’ placed under the bottom of a window
+displaying the text of this Licence or by affirming consent in any other similar way, in accordance with the rules of
+applicable law. Clicking on that icon indicates your clear and irrevocable acceptance of this Licence and all of its terms
+and conditions.
+Similarly, you irrevocably accept this Licence and all of its terms and conditions by exercising any rights granted to You
+by Article 2 of this Licence, such as the use of the Work, the creation by You of a Derivative Work or the Distribution
+or Communication by You of the Work or copies thereof.
+
+11.Information to the public
+In case of any Distribution or Communication of the Work by means of electronic communication by You (for example,
+by offering to download the Work from a remote location) the distribution channel or media (for example, a website)
+must at least provide to the public the information requested by the applicable law regarding the Licensor, the Licence
+and the way it may be accessible, concluded, stored and reproduced by the Licensee.
+
+12.Termination of the Licence
+The Licence and the rights granted hereunder will terminate automatically upon any breach by the Licensee of the terms
+of the Licence.
+Such a termination will not terminate the licences of any person who has received the Work from the Licensee under
+the Licence, provided such persons remain in full compliance with the Licence.
+
+13.Miscellaneous
+Without prejudice of Article 9 above, the Licence represents the complete agreement between the Parties as to the
+Work.
+If any provision of the Licence is invalid or unenforceable under applicable law, this will not affect the validity or
+enforceability of the Licence as a whole. Such provision will be construed or reformed so as necessary to make it valid
+and enforceable.
+The European Commission may publish other linguistic versions or new versions of this Licence or updated versions of
+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.
+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.
+
+14.Jurisdiction
+Without prejudice to specific agreement between parties,
+— 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
+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
+the exclusive jurisdiction of the competent court where the Licensor resides or conducts its primary business.
+
+15.Applicable Law
+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,
+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
+a European Union Member State.
+
+
+                                                         Appendix
+
+‘Compatible Licences’ according to Article 5 EUPL are:
+— GNU General Public License (GPL) v. 2, v. 3
+— GNU Affero General Public License (AGPL) v. 3
+— Open Software License (OSL) v. 2.1, v. 3.0
+— Eclipse Public License (EPL) v. 1.0
+— CeCILL v. 2.0, v. 2.1
+— Mozilla Public Licence (MPL) v. 2
+— 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
+— 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+).
+
+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
+covered Source Code from exclusive appropriation.
+All other changes or additions to this Appendix require the production of a new EUPL version.

README.md

@@ -1,17 +1,17 @@
-# reactor
-
-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.
-
-Key Features:
-
-Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
-ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
-Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
-Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves
-Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
-Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
-Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
-Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.
-
+# reactor
+
+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.
+
+Key Features:
+
+Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
+ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
+Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
+Oxygen Transfer: Saturation-limited O2 transfer with Fick's law slowdown effects and solubility curves
+Real-time Kinetics: Continuous biological reaction rate calculations with configurable time acceleration
+Weighted Averaging: Volume-based concentration mixing for accurate mass balance calculations
+Child Registration: Integration with diffuser systems and upstream/downstream reactor networks
+Supports complex biological treatment train modeling with temperature compensation, sludge calculations, and comprehensive process monitoring for wastewater treatment plant optimization and regulatory compliance.
+

additional_nodes/recirculation-pump.html

@@ -1,57 +1,57 @@
-<script type="text/javascript">
-    RED.nodes.registerType("recirculation-pump", {
-        category: "WWTP",
-        color: "#e4a363",
-        defaults: {
-            name: { value: "" },
-            F2: { value: 0, required: true },
-            inlet: { value: 1, required: true }
-        },
-        inputs: 1,
-        outputs: 2,
-        outputLabels: ["Main effluent", "Recirculation effluent"],
-        icon: "font-awesome/fa-random",
-        label: function() {
-            return this.name || "Recirculation pump";
-        },
-        oneditprepare: function() {
-            $("#node-input-F2").typedInput({
-                type:"num",
-                types:["num"]
-            });
-            $("#node-input-inlet").typedInput({
-                type:"num",
-                types:["num"]
-            });
-        },
-        oneditsave: function() {
-            let debit = parseFloat($("#node-input-F2").typedInput("value"));
-            if (isNaN(debit) || debit < 0) {
-                RED.notify("Debit is not set correctly", {type: "error"});
-            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
-        }
-    });
-</script>
-
-<script type="text/html" data-template-name="recirculation-pump">
-    <div class="form-row">
-        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
-        <input type="text" id="node-input-name" placeholder="Name">
-    </div>
-    <div class="form-row">
-        <label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label>
-        <input type="text" id="node-input-F2" placeholder="m3 s-1">
-    </div>
-    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
-</script>
-
-<script type="text/html" data-help-name="recirculation-pump">
-    <p>Recirculation-pump for splitting streams</p>
-</script>
+<script type="text/javascript">
+    RED.nodes.registerType("recirculation-pump", {
+        category: "WWTP",
+        color: "#e4a363",
+        defaults: {
+            name: { value: "" },
+            F2: { value: 0, required: true },
+            inlet: { value: 1, required: true }
+        },
+        inputs: 1,
+        outputs: 2,
+        outputLabels: ["Main effluent", "Recirculation effluent"],
+        icon: "font-awesome/fa-random",
+        label: function() {
+            return this.name || "Recirculation pump";
+        },
+        oneditprepare: function() {
+            $("#node-input-F2").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-inlet").typedInput({
+                type:"num",
+                types:["num"]
+            });
+        },
+        oneditsave: function() {
+            let debit = parseFloat($("#node-input-F2").typedInput("value"));
+            if (isNaN(debit) || debit < 0) {
+                RED.notify("Debit is not set correctly", {type: "error"});
+            }
+            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
+            if (inlet < 1) {
+                RED.notify("Number of inlets not set correctly", {type: "error"});
+            }
+        }
+    });
+</script>
+
+<script type="text/html" data-template-name="recirculation-pump">
+    <div class="form-row">
+        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
+        <input type="text" id="node-input-name" placeholder="Name">
+    </div>
+    <div class="form-row">
+        <label for="node-input-F2"><i class="fa fa-tag"></i> Recirculation debit [m3 d-1]</label>
+        <input type="text" id="node-input-F2" placeholder="m3 s-1">
+    </div>
+    <div class="form-row">
+        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet recirculation</label>
+        <input type="text" id="node-input-inlet" placeholder="#">
+    </div>
+</script>
+
+<script type="text/html" data-help-name="recirculation-pump">
+    <p>Recirculation-pump for splitting streams</p>
+</script>

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">
-    RED.nodes.registerType("settling-basin", {
-        category: "WWTP",
-        color: "#e4a363",
-        defaults: {
-            name: { value: "" },
-            TS_set: { value: 0.1, required: true },
-            inlet: { value: 1, required: true }
-        },
-        inputs: 1,
-        outputs: 2,
-        outputLabels: ["Main effluent", "Sludge effluent"],
-        icon: "font-awesome/fa-random",
-        label: function() {
-            return this.name || "Settling basin";
-        },
-        oneditprepare: function() {
-            $("#node-input-TS_set").typedInput({
-                type:"num",
-                types:["num"]
-            });
-            $("#node-input-inlet").typedInput({
-                type:"num",
-                types:["num"]
-            });
-        },
-        oneditsave: function() {
-            let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
-            if (isNaN(TS_set) || TS_set < 0) {
-                RED.notify("TS is not set correctly", {type: "error"});
-            }
-            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
-            if (inlet < 1) {
-                RED.notify("Number of inlets not set correctly", {type: "error"});
-            }
-        }
-    });
-</script>
-
-<script type="text/html" data-template-name="settling-basin">
-    <div class="form-row">
-        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
-        <input type="text" id="node-input-name" placeholder="Name">
-    </div>
-    <div class="form-row">
-        <label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label>
-        <input type="text" id="node-input-TS_set" placeholder="">
-    </div>
-    <div class="form-row">
-        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
-        <input type="text" id="node-input-inlet" placeholder="#">
-    </div>
-</script>
-
-<script type="text/html" data-help-name="settling-basin">
-    <p>Settling tank</p>
-</script>
+<script type="text/javascript">
+    RED.nodes.registerType("settling-basin", {
+        category: "WWTP",
+        color: "#e4a363",
+        defaults: {
+            name: { value: "" },
+            TS_set: { value: 0.1, required: true },
+            inlet: { value: 1, required: true }
+        },
+        inputs: 1,
+        outputs: 2,
+        outputLabels: ["Main effluent", "Sludge effluent"],
+        icon: "font-awesome/fa-random",
+        label: function() {
+            return this.name || "Settling basin";
+        },
+        oneditprepare: function() {
+            $("#node-input-TS_set").typedInput({
+                type:"num",
+                types:["num"]
+            });
+            $("#node-input-inlet").typedInput({
+                type:"num",
+                types:["num"]
+            });
+        },
+        oneditsave: function() {
+            let TS_set = parseFloat($("#node-input-TS_set").typedInput("value"));
+            if (isNaN(TS_set) || TS_set < 0) {
+                RED.notify("TS is not set correctly", {type: "error"});
+            }
+            let inlet = parseInt($("#node-input-n_inlets").typedInput("value"));
+            if (inlet < 1) {
+                RED.notify("Number of inlets not set correctly", {type: "error"});
+            }
+        }
+    });
+</script>
+
+<script type="text/html" data-template-name="settling-basin">
+    <div class="form-row">
+        <label for="node-input-name"><i class="fa fa-tag"></i> Name</label>
+        <input type="text" id="node-input-name" placeholder="Name">
+    </div>
+    <div class="form-row">
+        <label for="node-input-TS_set"><i class="fa fa-tag"></i> Total Solids set point [g m-3]</label>
+        <input type="text" id="node-input-TS_set" placeholder="">
+    </div>
+    <div class="form-row">
+        <label for="node-input-inlet"><i class="fa fa-tag"></i> Assigned inlet return line</label>
+        <input type="text" id="node-input-inlet" placeholder="#">
+    </div>
+</script>
+
+<script type="text/html" data-help-name="settling-basin">
+    <p>Settling tank</p>
+</script>

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:

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

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":[]}
+]

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":[]}
+]

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":[]}
+]

package-lock.json

@@ -1,119 +1,119 @@
-{
-  "name": "reactor",
-  "version": "0.0.1",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "reactor",
-      "version": "0.0.1",
-      "license": "SEE LICENSE",
-      "dependencies": {
-        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
-        "mathjs": "^14.5.2"
-      }
-    },
-    "node_modules/@babel/runtime": {
-      "version": "7.28.4",
-      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
-      "integrity": "sha512-Q/N6JNWvIvPnLDvjlE1OUBLPQHH6l3CltCEsHIujp45zQUSSh8K+gHnaEX45yAT1nyngnINhvWtzN+Nb9D8RAQ==",
-      "license": "MIT",
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/complex.js": {
-      "version": "2.4.2",
-      "resolved": "https://registry.npmjs.org/complex.js/-/complex.js-2.4.2.tgz",
-      "integrity": "sha512-qtx7HRhPGSCBtGiST4/WGHuW+zeaND/6Ld+db6PbrulIB1i2Ev/2UPiqcmpQNPSyfBKraC0EOvOKCB5dGZKt3g==",
-      "license": "MIT",
-      "engines": {
-        "node": "*"
-      },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/rawify"
-      }
-    },
-    "node_modules/decimal.js": {
-      "version": "10.6.0",
-      "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
-      "integrity": "sha512-YpgQiITW3JXGntzdUmyUR1V812Hn8T1YVXhCu+wO3OpS4eU9l4YdD3qjyiKdV6mvV29zapkMeD390UVEf2lkUg==",
-      "license": "MIT"
-    },
-    "node_modules/escape-latex": {
-      "version": "1.2.0",
-      "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz",
-      "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==",
-      "license": "MIT"
-    },
-    "node_modules/fraction.js": {
-      "version": "5.3.4",
-      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
-      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
-      "license": "MIT",
-      "engines": {
-        "node": "*"
-      },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/rawify"
-      }
-    },
-    "node_modules/generalFunctions": {
-      "version": "1.0.0",
-      "resolved": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
-      "license": "SEE LICENSE"
-    },
-    "node_modules/javascript-natural-sort": {
-      "version": "0.7.1",
-      "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",
-      "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==",
-      "license": "MIT"
-    },
-    "node_modules/mathjs": {
-      "version": "14.8.0",
-      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
-      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@babel/runtime": "^7.26.10",
-        "complex.js": "^2.2.5",
-        "decimal.js": "^10.4.3",
-        "escape-latex": "^1.2.0",
-        "fraction.js": "^5.2.1",
-        "javascript-natural-sort": "^0.7.1",
-        "seedrandom": "^3.0.5",
-        "tiny-emitter": "^2.1.0",
-        "typed-function": "^4.2.1"
-      },
-      "bin": {
-        "mathjs": "bin/cli.js"
-      },
-      "engines": {
-        "node": ">= 18"
-      }
-    },
-    "node_modules/seedrandom": {
-      "version": "3.0.5",
-      "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz",
-      "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==",
-      "license": "MIT"
-    },
-    "node_modules/tiny-emitter": {
-      "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz",
-      "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==",
-      "license": "MIT"
-    },
-    "node_modules/typed-function": {
-      "version": "4.2.1",
-      "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz",
-      "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==",
-      "license": "MIT",
-      "engines": {
-        "node": ">= 18"
-      }
-    }
-  }
-}
+{
+  "name": "reactor",
+  "version": "0.0.1",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "reactor",
+      "version": "0.0.1",
+      "license": "SEE LICENSE",
+      "dependencies": {
+        "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
+        "mathjs": "^14.5.2"
+      }
+    },
+    "node_modules/@babel/runtime": {
+      "version": "7.28.4",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.28.4.tgz",
+      "integrity": "sha512-Q/N6JNWvIvPnLDvjlE1OUBLPQHH6l3CltCEsHIujp45zQUSSh8K+gHnaEX45yAT1nyngnINhvWtzN+Nb9D8RAQ==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/complex.js": {
+      "version": "2.4.2",
+      "resolved": "https://registry.npmjs.org/complex.js/-/complex.js-2.4.2.tgz",
+      "integrity": "sha512-qtx7HRhPGSCBtGiST4/WGHuW+zeaND/6Ld+db6PbrulIB1i2Ev/2UPiqcmpQNPSyfBKraC0EOvOKCB5dGZKt3g==",
+      "license": "MIT",
+      "engines": {
+        "node": "*"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/rawify"
+      }
+    },
+    "node_modules/decimal.js": {
+      "version": "10.6.0",
+      "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.6.0.tgz",
+      "integrity": "sha512-YpgQiITW3JXGntzdUmyUR1V812Hn8T1YVXhCu+wO3OpS4eU9l4YdD3qjyiKdV6mvV29zapkMeD390UVEf2lkUg==",
+      "license": "MIT"
+    },
+    "node_modules/escape-latex": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz",
+      "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==",
+      "license": "MIT"
+    },
+    "node_modules/fraction.js": {
+      "version": "5.3.4",
+      "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-5.3.4.tgz",
+      "integrity": "sha512-1X1NTtiJphryn/uLQz3whtY6jK3fTqoE3ohKs0tT+Ujr1W59oopxmoEh7Lu5p6vBaPbgoM0bzveAW4Qi5RyWDQ==",
+      "license": "MIT",
+      "engines": {
+        "node": "*"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/rawify"
+      }
+    },
+    "node_modules/generalFunctions": {
+      "version": "1.0.0",
+      "resolved": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git#efc97d6cd17399391b011298e47e8c1b1599592d",
+      "license": "SEE LICENSE"
+    },
+    "node_modules/javascript-natural-sort": {
+      "version": "0.7.1",
+      "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz",
+      "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==",
+      "license": "MIT"
+    },
+    "node_modules/mathjs": {
+      "version": "14.8.0",
+      "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-14.8.0.tgz",
+      "integrity": "sha512-DN4wmAjNzFVJ9vHqpAJ3vX0UF306u/1DgGKh7iVPuAFH19JDRd9NAaQS764MsKbSwDB6uBSkQEmgVmKdgYaCoQ==",
+      "license": "Apache-2.0",
+      "dependencies": {
+        "@babel/runtime": "^7.26.10",
+        "complex.js": "^2.2.5",
+        "decimal.js": "^10.4.3",
+        "escape-latex": "^1.2.0",
+        "fraction.js": "^5.2.1",
+        "javascript-natural-sort": "^0.7.1",
+        "seedrandom": "^3.0.5",
+        "tiny-emitter": "^2.1.0",
+        "typed-function": "^4.2.1"
+      },
+      "bin": {
+        "mathjs": "bin/cli.js"
+      },
+      "engines": {
+        "node": ">= 18"
+      }
+    },
+    "node_modules/seedrandom": {
+      "version": "3.0.5",
+      "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz",
+      "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==",
+      "license": "MIT"
+    },
+    "node_modules/tiny-emitter": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz",
+      "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==",
+      "license": "MIT"
+    },
+    "node_modules/typed-function": {
+      "version": "4.2.1",
+      "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz",
+      "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 18"
+      }
+    }
+  }
+}

package.json

@@ -1,33 +1,33 @@
-{
-  "name": "reactor",
-  "version": "0.0.1",
-  "description": "Implementation of the asm3 model for Node-Red",
-  "repository": {
-    "type": "git",
-    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
-  },
-  "keywords": [
-    "asm3",
-    "activated sludge",
-    "wastewater",
-    "biological model",
-    "node-red"
-  ],
-  "license": "SEE LICENSE",
-  "author": "P.R. van der Wilt",
-  "main": "reactor.js",
+{
+  "name": "reactor",
+  "version": "0.0.1",
+  "description": "Implementation of the asm3 model for Node-Red",
+  "repository": {
+    "type": "git",
+    "url": "https://gitea.centraal.wbd-rd.nl/RnD/reactor.git"
+  },
+  "keywords": [
+    "asm3",
+    "activated sludge",
+    "wastewater",
+    "biological model",
+    "node-red"
+  ],
+  "license": "SEE LICENSE",
+  "author": "P.R. van der Wilt",
+  "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": {
-    "nodes": {
-      "reactor": "reactor.js",
-      "recirculation-pump": "additional_nodes/recirculation-pump.js",
-      "settling-basin": "additional_nodes/settling-basin.js"
-    }
-  },
-  "dependencies": {
-    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
-    "mathjs": "^14.5.2"
-  }
-}
+  "node-red": {
+    "nodes": {
+      "reactor": "reactor.js",
+      "recirculation-pump": "additional_nodes/recirculation-pump.js",
+      "settling-basin": "additional_nodes/settling-basin.js"
+    }
+  },
+  "dependencies": {
+    "generalFunctions": "git+https://gitea.centraal.wbd-rd.nl/RnD/generalFunctions.git",
+    "mathjs": "^14.5.2"
+  }
+}

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",
-        color: "#c4cce0",
+        category: "EVOLV",
+        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) {
-                window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
+            if (window.EVOLV?.nodes?.reactor?.positionMenu?.saveEditor) {
+                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>

reactor.js

@@ -1,26 +1,26 @@
-const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
-const nodeClass = require('./src/nodeClass.js'); // node class
-const { MenuManager } = require('generalFunctions');
-
-
-module.exports = function (RED) {
-    // Register the node type
-    RED.nodes.registerType(nameOfNode, function (config) {
-        // Initialize the Node-RED node first
-        RED.nodes.createNode(this, config);
-        // Then create your custom class and attach it
-        this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
-    });
-
-    const menuMgr = new MenuManager();
-
-    // Serve /advancedReactor/menu.js
-    RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
-        try {
-            const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
-            res.type('application/javascript').send(script);
-        } catch (err) {
-            res.status(500).send(`// Error generating menu: ${err.message}`);
-        }
-    });
-};
+const nameOfNode = "reactor"; // name of the node, should match file name and node type in Node-RED
+const nodeClass = require('./src/nodeClass.js'); // node class
+const { MenuManager } = require('generalFunctions');
+
+
+module.exports = function (RED) {
+    // Register the node type
+    RED.nodes.registerType(nameOfNode, function (config) {
+        // Initialize the Node-RED node first
+        RED.nodes.createNode(this, config);
+        // Then create your custom class and attach it
+        this.nodeClass = new nodeClass(config, RED, this, nameOfNode);
+    });
+
+    const menuMgr = new MenuManager();
+
+    // Serve /advancedReactor/menu.js
+    RED.httpAdmin.get(`/${nameOfNode}/menu.js`, (req, res) => {
+        try {
+            const script = menuMgr.createEndpoint(nameOfNode, ['logger', 'position']);
+            res.type('application/javascript').send(script);
+        } catch (err) {
+            res.status(500).send(`// Error generating menu: ${err.message}`);
+        }
+    });
+};

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();
@@ -30,59 +48,56 @@ class nodeClass {
      */
     _attachInputHandler() {
         this.node.on('input', (msg, send, done) => {
-
-            switch (msg.topic) {
-                case "clock":
-                    this.source.updateState(msg.timestamp);
-                    send([msg, null, null]);
-                    break;
-                case "Fluent":
-                    this.source.setInfluent = msg;
-                    break;
-                case "OTR":
-                    this.source.setOTR = msg;
-                    break;
-                case "Temperature":
-                    this.source.setTemperature = msg;
-                    break;
-                case "Dispersion":
-                    this.source.setDispersion = msg;
-                    break;
-                case 'registerChild':
-                    // Register this node as a parent of the child node
-                    const childId = msg.payload;
-                    const childObj = this.RED.nodes.getNode(childId); 
-                    this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
-                    break;
-                default:
-                    console.log("Unknown topic: " + msg.topic);
+            try {
+                switch (msg.topic) {
+                    case "clock":
+                        this.source.updateState(msg.timestamp);
+                        send([msg, null, null]);
+                        break;
+                    case "Fluent":
+                        this.source.setInfluent = msg;
+                        break;
+                    case "OTR":
+                        this.source.setOTR = msg;
+                        break;
+                    case "Temperature":
+                        this.source.setTemperature = msg;
+                        break;
+                    case "Dispersion":
+                        this.source.setDispersion = msg;
+                        break;
+                    case 'registerChild': {
+                        const childId = msg.payload;
+                        const childObj = this.RED.nodes.getNode(childId);
+                        if (!childObj || !childObj.source) {
+                            this.source?.logger?.warn(`registerChild skipped: missing child/source for id=${childId}`);
+                            break;
+                        }
+                        this.source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
+                        break;
+                    }
+                    default:
+                        this.source?.logger?.warn(`Unknown topic: ${msg.topic}`);
+                }
+            } catch (error) {
+                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) {
-        this.config = {
-            general: {
-                name: uiConfig.name || this.name,
-                id: this.node.id,
-                unit: null,
-                logging: {
-                    enabled: uiConfig.enableLog,
-                    logLevel: uiConfig.logLevel
-                }
-            },
-            functionality: {
-                positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
-                softwareType: "reactor" // should be set in config manager
-            },
+        const cfgMgr = new configManager();
+
+        // Build config: base sections + reactor-specific domain config
+        this.config = cfgMgr.buildConfig('reactor', uiConfig, this.node.id, {
             reactor_type: uiConfig.reactor_type,
             volume: parseFloat(uiConfig.volume),
             length: parseFloat(uiConfig.length),
@@ -105,8 +120,9 @@ 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
+        });
     }
 
     /**
@@ -137,7 +153,8 @@ class nodeClass {
                 new_reactor = new Reactor_PFR(this.config);
                 break;
             default:
-                console.warn("Unknown reactor type: " + uiConfig.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
@@ -151,15 +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;

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 = {
@@ -12,7 +12,6 @@ const math = create(all, mathConfig);
 
 const S_O_INDEX = 0;
 const NUM_SPECIES = 13;
-const BC_PADDING = 2;
 const DEBUG = false;
 
 class Reactor {
@@ -28,10 +27,6 @@ class Reactor {
     this.measurements = new MeasurementContainer();
     this.upstreamReactor = null;
     this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
-    this.parent = []; // Gets assigned via child registration
-
-    this.upstreamReactor = null;
-    this.downstreamReactor = null;
 
     this.asm = new ASM3();
 
@@ -46,7 +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 = 100; // speed up factor for simulation, 60 means 1 minute per simulated second
+    this.speedUpFactor = config.speedUpFactor ?? 1; // speed up factor for simulation
   }
 
   /**
@@ -67,6 +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.
@@ -78,6 +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].
@@ -89,6 +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.
@@ -118,18 +156,23 @@ class Reactor {
     }
   }
 
-  _connectMeasurement(measurementChild) {
-    if (!measurementChild) {
+  _connectMeasurement(measurement) {
+    if (!measurement) {
       this.logger.warn("Invalid measurement provided.");
       return;
     }
 
-    const position = measurementChild.config.functionality.positionVsParent;
-    const measurementType = measurementChild.config.asset.type;
+    let position;
+    if (measurement.config.functionality.distance !== 'undefined') {
+      position = measurement.config.functionality.distance;
+    } else {
+      position = measurement.config.functionality.positionVsParent;
+    }
+    const measurementType = measurement.config.asset.type;
     const eventName = `${measurementType}.measured.${position}`;
 
     // Register event listener for measurement updates
-    measurementChild.measurements.emitter.on(eventName, (eventData) => {
+    measurement.measurements.emitter.on(eventName, (eventData) => {
       this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
 
       // Store directly in parent's measurement container
@@ -138,33 +181,32 @@ class Reactor {
         .variant("measured")
         .position(position)
         .value(eventData.value, eventData.timestamp, eventData.unit);
-      
+
       this._updateMeasurement(measurementType, eventData.value, position, eventData);
     });
   }
 
 
-  _connectReactor(reactorChild) {
-    if (!reactorChild) {
+  _connectReactor(reactor) {
+    if (!reactor) {
       this.logger.warn("Invalid reactor provided.");
       return;
     }
 
-    this.upstreamReactor = reactorChild;
-    reactorChild.downstreamReactor = this;
+    this.upstreamReactor = reactor;
 
-    reactorChild.emitter.on("stateChange", (data) => {
+    reactor.emitter.on("stateChange", (data) => {
       this.logger.debug(`State change of upstream reactor detected.`);
       this.updateState(data);
     });
   }
 
-  
-  _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;
@@ -221,7 +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");
@@ -246,21 +288,29 @@ class Reactor_PFR extends Reactor {
 
     this.alpha = config.alpha;
 
-    this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
-    this.extendedState = Array.from(Array(this.n_x + 2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
-
-    // initialise extended state
-    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+    this.state = Array.from(Array(this.n_x), () => config.initialState.slice())
 
     this.D = 0.0; // axial dispersion [m2 d-1]
 
-    this.D_op = this._makeDoperator();
+    this.D_op = this._makeDoperator(true, true);
     assertNoNaN(this.D_op, "Derivative operator");
 
     this.D2_op = this._makeD2operator();
     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].
@@ -274,7 +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) {
@@ -292,26 +342,25 @@ class Reactor_PFR extends Reactor {
    * @returns {Array} - New reactor state.
    */
   tick(time_step) {
-    this._applyBoundaryConditions();
-
-    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
-    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.extendedState);
-    const reaction = this.extendedState.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
-    const transfer = Array.from(Array(this.n_x+2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
+    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.state);
+    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.state);
+    const reaction = this.state.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
+    const transfer = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
 
     if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
-      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+      for (let i = 1; i < this.n_x - 1; i++) {
         transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
       }
     } else {
-    for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
-        transfer[i][S_O_INDEX] = this._calcOTR(this.extendedState[i][S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
+    for (let i = 1; i < this.n_x - 1; i++) {
+        transfer[i][S_O_INDEX] = this._calcOTR(this.state[i][S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
       }
     }
 
-    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
+    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
 
     const stateNew = math.add(this.state, dC_total);
+    this._applyBoundaryConditions(stateNew);
 
     if (DEBUG) {
       assertNoNaN(dispersion, "dispersion");
@@ -321,16 +370,23 @@ class Reactor_PFR extends Reactor {
       assertNoNaN(stateNew, "new state post BC");
     }
 
-    this.state = this._arrayClip2Zero(stateNew);
-    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
     return stateNew;
   }
 
   _updateMeasurement(measurementType, value, position, context) {
     switch(measurementType) {
       case "quantity (oxygen)":
-        let grid_pos = Math.round(context.distance / this.config.length * this.n_x);
-        this.state[grid_pos][S_O_INDEX] = value; // naive approach for reconciling measurements and simulation
+        if (!Number.isFinite(position) || !Number.isFinite(value) || this.config.length <= 0) {
+          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);
@@ -341,51 +397,57 @@ class Reactor_PFR extends Reactor {
    * Apply boundary conditions to the reactor state.
    *  for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux
    *  for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
+   * @param {Array} state - Current reactor state without enforced BCs.
    */
-  _applyBoundaryConditions() {
-    if (this.upstreamReactor) {
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
-      }
+  _applyBoundaryConditions(state) {
+    if (math.sum(this.Fs) > 0) { // Danckwerts BC
+      const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
+      const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
+      state[0] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, state[1])));
     } else {
-      if (math.sum(this.Fs) > 0) { // Danckwerts BC
-        const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
-        const BC_dispersion_term = (1-this.alpha)*this.D*this.A/(math.sum(this.Fs)*this.d_x);
-        this.extendedState[BC_PADDING] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, this.extendedState[BC_PADDING+1])));
-        this.extendedState[BC_PADDING-1] = math.add(math.multiply(2, this.extendedState[BC_PADDING]), math.multiply(-2, this.extendedState[BC_PADDING+2]), this.extendedState[BC_PADDING+3]);
-      } else {
-        for (let i = 0; i < BC_PADDING; i++) {
-          this.extendedState[i] = this.extendedState[BC_PADDING];
-        }
-      }
-    }
-
-    if (this.downstreamReactor) {
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[this.n_x+BC_PADDING+i] = this.downstreamReactor.state[i];
-      }
-    } else {
-      // Neumann BC (no flux)
-      for (let i = 0; i < BC_PADDING; i++) {
-        this.extendedState[BC_PADDING+this.n_x+i] = this.extendedState.at(-1-BC_PADDING);
-      }
+      state[0] = state[1];
     }
+    // Neumann BC (no flux)
+    state[this.n_x-1] = state[this.n_x-2];
   }
 
   /**
    * Create finite difference first derivative operator.
+   * @param {boolean} central - Use central difference scheme if true, otherwise use upwind scheme.
+   * @param {boolean} higher_order - Use higher order scheme if true, otherwise use first order scheme.
    * @returns {Array} - First derivative operator matrix.
    */
-  _makeDoperator() { // create gradient operator
-    const D_size = this.n_x+2*BC_PADDING;
-    const I = math.resize(math.diag(Array(D_size).fill(1/12), -2), [D_size, D_size]);
-    const A = math.resize(math.diag(Array(D_size).fill(-2/3), -1), [D_size, D_size]);
-    const B = math.resize(math.diag(Array(D_size).fill(2/3), 1), [D_size, D_size]);
-    const C = math.resize(math.diag(Array(D_size).fill(-1/12), 2), [D_size, D_size]);
-    const D = math.add(I, A, B, C);
-    // set by BCs elsewhere
-    D.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
-    return D;
+  _makeDoperator(central = false, higher_order = false) { // create gradient operator
+    if (higher_order) {
+      if (central) {
+        const I = math.resize(math.diag(Array(this.n_x).fill(1/12), -2), [this.n_x, this.n_x]);
+        const A = math.resize(math.diag(Array(this.n_x).fill(-2/3), -1), [this.n_x, this.n_x]);
+        const B = math.resize(math.diag(Array(this.n_x).fill(2/3), 1), [this.n_x, this.n_x]);
+        const C = math.resize(math.diag(Array(this.n_x).fill(-1/12), 2), [this.n_x, this.n_x]);
+        const D = math.add(I, A, B, C);
+        const NearBoundary = Array(this.n_x).fill(0.0);
+        NearBoundary[0] = -1/4;
+        NearBoundary[1] = -5/6;
+        NearBoundary[2] = 3/2;
+        NearBoundary[3] = -1/2;
+        NearBoundary[4] = 1/12;
+        D[1] = NearBoundary;
+        NearBoundary.reverse();
+        D[this.n_x-2] = math.multiply(-1, NearBoundary);
+        D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
+        D[this.n_x-1] = Array(this.n_x).fill(0);
+        return D;
+      } else {
+        throw new Error("Upwind higher order method not implemented! Use central scheme instead.");
+      }
+    } else {
+      const I = math.resize(math.diag(Array(this.n_x).fill(1 / (1+central)), central), [this.n_x, this.n_x]);
+      const A = math.resize(math.diag(Array(this.n_x).fill(-1 / (1+central)), -1), [this.n_x, this.n_x]);
+      const D = math.add(I, A);
+      D[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
+      D[this.n_x-1] = Array(this.n_x).fill(0);
+      return D;
+    }
   }
 
   /**
@@ -393,13 +455,12 @@ class Reactor_PFR extends Reactor {
    * @returns {Array} - Second derivative operator matrix.
    */
   _makeD2operator() { // create the central second derivative operator
-    const D_size = this.n_x+2*BC_PADDING;
-    const I = math.diag(Array(D_size).fill(-2), 0);
-    const A = math.resize(math.diag(Array(D_size).fill(1), 1), [D_size, D_size]);
-    const B = math.resize(math.diag(Array(D_size).fill(1), -1), [D_size, D_size]);
+    const I = math.diag(Array(this.n_x).fill(-2), 0);
+    const A = math.resize(math.diag(Array(this.n_x).fill(1), 1), [this.n_x, this.n_x]);
+    const B = math.resize(math.diag(Array(this.n_x).fill(1), -1), [this.n_x, this.n_x]);
     const D2 = math.add(I, A, B);
-    // set by BCs elsewhere
-    D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
+    D2[0] = Array(this.n_x).fill(0); // set by BCs elsewhere
+    D2[this.n_x - 1] = Array(this.n_x).fill(0);
     return D2;
   }
 }
@@ -417,4 +478,4 @@ module.exports = { Reactor_CSTR, Reactor_PFR };
 // while (N < 5000) {
 //     console.log(Reactor.tick(0.001));
 //     N += 1;
-// }
+// }

src/utils.js

@@ -1,18 +1,18 @@
-/**
- * Assert that no NaN values are present in an array.
- * @param {Array} arr 
- * @param {string} label 
- */
-function assertNoNaN(arr, label = "array") {
-    if (Array.isArray(arr)) {
-        for (const el of arr) {
-            assertNoNaN(el, label);
-        }
-    } else {
-        if (Number.isNaN(arr)) {
-            throw new Error(`NaN detected in ${label}!`);
-        }
-    }
-}
-
+/**
+ * Assert that no NaN values are present in an array.
+ * @param {Array} arr 
+ * @param {string} label 
+ */
+function assertNoNaN(arr, label = "array") {
+    if (Array.isArray(arr)) {
+        for (const el of arr) {
+            assertNoNaN(el, label);
+        }
+    } else {
+        if (Number.isNaN(arr)) {
+            throw new Error(`NaN detected in ${label}!`);
+        }
+    }
+}
+
 module.exports = { assertNoNaN };

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

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);
+});

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);
+});

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));
+});

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');
+});

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']);
+});

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));
+});

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');
+});

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)`);
+});

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');
+  });
+});

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();
+  });
+});

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);
+});

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' },
+      () => {},
+      () => {},
+    );
+  });
+});

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);
+});

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);
+});

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);
+});

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,
+};

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);
+});

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);
+});

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]);
+});

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);
+  }
+});

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);
+});

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));
+});

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