Refactor measurement position assignment and update grid position calculation in Reactor classes to align with new generalFunctions

.gitignore

@@ -1,136 +1,136 @@
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CLAUDE.md

@@ -1,40 +0,0 @@
-# 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).
-
-## Folder & File Layout
-
-Every per-node file MUST use the folder name (`reactor`) **exactly**, case-sensitive. Full rule: [`.claude/rules/node-architecture.md`](https://gitea.wbd-rd.nl/RnD/EVOLV/src/branch/development/.claude/rules/node-architecture.md) in the EVOLV superproject.
-
-| Path | Required name |
-|---|---|
-| Entry file | `reactor.js` |
-| Editor HTML | `reactor.html` |
-| Node adapter | `src/nodeClass.js` |
-| Domain logic | `src/specificClass.js` |
-| Editor JS modules | `src/editor/*.js` (extract when inline editor JS exceeds ~50 lines) |
-| Tests | `test/{basic,integration,edge}/*.test.js` |
-| Example flows | `examples/*.flow.json` |
-
-
-When adding new files, read the rule above first to avoid drift.

CONTRACT.md

@@ -1,51 +0,0 @@
-# reactor — Contract
-
-Hand-maintained for Phase 6; the `## Inputs` table is generated from
-`src/commands/index.js` (see Phase 9 generator). Keep ≤ 80 lines.
-
-## Inputs (msg.topic on Port 0)
-
-| Canonical | Aliases (deprecated) | Payload | Effect |
-|---|---|---|---|
-| `data.clock` | `clock` | `msg.timestamp` (ms since epoch) | Calls `source.updateState(timestamp)` — advances the ASM kinetics integrator by `n_iter` time steps that fit between `currentTime` and the supplied timestamp (scaled by `speedUpFactor`). |
-| `data.fluent` | `Fluent` | `{ inlet: number, F: number, C: number[13] }` | Writes the per-inlet flow rate (`F`, m³/d) and concentration vector (`C`) into `engine.Fs[inlet]` / `engine.Cs_in[inlet]`. |
-| `data.otr` | `OTR` | numeric | Sets the externally-supplied oxygen transfer rate (used when `kla` is NaN). |
-| `data.temperature` | `Temperature` | numeric or `{ value: number }` | Sets `engine.temperature` (°C). Non-numeric payloads are warned and ignored. |
-| `data.dispersion` | `Dispersion` | numeric | PFR only — sets the axial dispersion coefficient `D` (m²/d). |
-| `child.register` | `registerChild` | child node id (string) | Looks up the sibling node via `RED.nodes.getNode(id)` and delegates to `source.childRegistrationUtils.registerChild` with `msg.positionVsParent`. |
-
-Aliases log a one-time deprecation warning the first time they fire.
-
-## Outputs (msg.topic on Port 0/1/2)
-
-- **Port 0 (process):** every tick emits the engine's effluent:
-  `{ topic: 'Fluent', payload: { inlet: 0, F, C: number[13] }, timestamp }`.
-  For a PFR an additional `{ topic: 'GridProfile', payload: { grid, n_x, d_x, length, species, timestamp } }`
-  message goes out on the same port before the effluent.
-- **Port 1 (InfluxDB telemetry):** formatted via `outputUtils.formatMsg(..., 'influxdb')`
-  from `getOutput()` — carries `flow_total`, `temperature`, and one field per ASM3
-  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`).
-- **Port 2 (registration):** at startup the node sends one
-  `{ topic: 'child.register', payload: <node.id>, positionVsParent, distance }`
-  to its parent.
-
-## Events emitted by `source.emitter`
-
-- `stateChange` — fires after every `updateState()` that advances the integrator.
-  Payload is the new `currentTime` (ms since epoch). Downstream reactors register
-  via `child.register` and subscribe to this event to pull the upstream
-  effluent on each advance.
-- `output-changed` — base notification fired by `updateState()` so the
-  BaseNodeAdapter pipeline pushes outputs (currently used only as a heartbeat;
-  effluent is emitted directly from the periodic tick).
-
-## Children accepted
-
-- `measurement` — subscribes to `<type>.measured.<position>` on the child's
-  `measurements.emitter`. Recognised reconciliations: `temperature.measured.atEquipment`
-  writes `engine.temperature`; PFR additionally honours
-  `quantity (oxygen).measured.<distance>` to reconcile dissolved-oxygen
-  concentration into the nearest grid cell.
-- `reactor` — registers as the upstream reactor; the downstream `updateState`
-  pulls the upstream effluent into `Fs[0]` / `Cs_in[0]` before integrating.

LICENSE

@@ -1,190 +1,190 @@
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+4.Limitations on copyright
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+
+5.Obligations of the Licensee
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+
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+Copyleft clause: If the Licensee distributes or communicates copies of the Original Works or Derivative Works, this
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+the Original Work is expressly distributed only under this version of the Licence — for example by communicating
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+
+Compatibility clause: If the Licensee Distributes or Communicates Derivative Works or copies thereof based upon both
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+
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+6.Chain of Authorship
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+8.Disclaimer of Liability
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+
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+
+11.Information to the public
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+
+12.Termination of the Licence
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+of the Licence.
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+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.
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+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

@@ -3,12 +3,13 @@ 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);
@@ -23,7 +24,6 @@ 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

@@ -3,12 +3,13 @@ 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;
@@ -40,7 +41,6 @@ module.exports = function(RED) {
 
                     send([msg_F1, msg_F2]);
                     break;
-                }
                 case "clock":
                     break;
                 default:

examples/README.md

@@ -1,8 +0,0 @@
-# reactor Example Flows
-
-Import-ready Node-RED examples for reactor.
-
-## Files
-- basic.flow.json
-- integration.flow.json
-- edge.flow.json

examples/basic.flow.json

@@ -1,6 +0,0 @@
-[
-  {"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

@@ -1,6 +0,0 @@
-[
-  {"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

@@ -1,6 +0,0 @@
-[
-  {"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

@@ -1,36 +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",
-  "scripts": {
-    "test": "node --test test/basic/*.test.js test/integration/*.test.js test/edge/*.test.js",
-    "wiki:contract":  "node ../generalFunctions/scripts/wikiGen.js contract  ./src/commands/index.js   --write ./wiki/Home.md",
-    "wiki:datamodel": "node ../generalFunctions/scripts/wikiGen.js datamodel ./src/specificClass.js     --write ./wiki/Home.md",
-    "wiki:all":       "npm run wiki:contract && npm run wiki:datamodel"
-  },
-  "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"
-  }
-}
+{
+  "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"
+  },
+  "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

@@ -1,19 +1,9 @@
-<!--
-| 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: "EVOLV",
-        color: "#50a8d9",
+        category: "WWTP",
+        color: "#c4cce0",
         defaults: {
             name: { value: "" },
             reactor_type: { value: "CSTR", required: true },
@@ -23,7 +13,7 @@
             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 },
@@ -35,13 +25,10 @@
             X_S_init: { value: 75., required: true },
             X_H_init: { value: 30., required: true },
             X_STO_init: { value: 0., required: true },
-            X_A_init: { value: 200, required: true },
+            X_A_init: { value: 0.001, required: true },
             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" },
@@ -52,7 +39,7 @@
         outputs: 3,
         inputLabels: ["input"],
         outputLabels: ["process", "dbase", "parent"],
-        icon: "font-awesome/fa-flask",
+        icon: "font-awesome/fa-recycle",
         label: function() {
             return this.name || "Reactor";
         },
@@ -118,10 +105,6 @@
                 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") {
@@ -137,8 +120,8 @@
             }
 
             // save position field
-            if (window.EVOLV?.nodes?.reactor?.positionMenu?.saveEditor) {
-                window.EVOLV.nodes.reactor.positionMenu.saveEditor(this);
+            if (window.EVOLV?.nodes?.measurement?.positionMenu?.saveEditor) {
+                window.EVOLV.nodes.rotatingMachine.positionMenu.saveEditor(this);
             }
 
             let volume = parseFloat($("#node-input-volume").typedInput("value"));
@@ -250,27 +233,6 @@
         <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/commands/handlers.js

@@ -1,25 +0,0 @@
-'use strict';
-
-// Reactor input handlers. Each receives (source, msg, ctx) where source is
-// the Reactor domain and ctx is { node, RED, send, logger }. The handlers
-// either forward to engine setters or drive a synchronous state update.
-
-exports.dataClock = (source, msg) => {
-  source.updateState(msg.timestamp ?? Date.now());
-};
-
-exports.dataFluent     = (source, msg) => { source.setInfluent    = msg; };
-exports.dataOTR        = (source, msg) => { source.setOTR         = msg; };
-exports.dataTemperature = (source, msg) => { source.setTemperature = msg; };
-exports.dataDispersion = (source, msg) => { source.setDispersion  = msg; };
-
-exports.childRegister = (source, msg, ctx) => {
-  const childId = msg.payload;
-  const RED = ctx?.RED;
-  const childObj = RED?.nodes?.getNode?.(childId);
-  if (!childObj || !childObj.source) {
-    source?.logger?.warn?.(`registerChild skipped: missing child/source for id=${childId}`);
-    return;
-  }
-  source.childRegistrationUtils.registerChild(childObj.source, msg.positionVsParent);
-};

src/commands/index.js

@@ -1,55 +0,0 @@
-'use strict';
-
-// reactor command registry. Canonical names follow CONTRACTS.md §1.
-// Legacy names (clock, Fluent, OTR, Temperature, Dispersion, registerChild)
-// stay as aliases — they log a one-time deprecation warning on first use
-// and are removed in Phase 7.
-
-const handlers = require('./handlers');
-
-module.exports = [
-  {
-    topic: 'data.clock',
-    aliases: ['clock'],
-    payloadSchema: { type: 'any' },
-    description: 'Push the simulation clock tick (timestamp / dt) to the ASM solver.',
-    handler: handlers.dataClock,
-  },
-  {
-    topic: 'data.fluent',
-    aliases: ['Fluent'],
-    payloadSchema: { type: 'object' },
-    // Compound payload `{F, C: [...]}` — registry-level units normalisation is
-    // skipped (the handler converts per-field internally).
-    description: 'Push the influent stream (payload: {F: flow m3/h, C: [concentrations mg/L]}).',
-    handler: handlers.dataFluent,
-  },
-  {
-    topic: 'data.otr',
-    aliases: ['OTR'],
-    payloadSchema: { type: 'any' },
-    description: 'Push the current oxygen-transfer rate into the reactor.',
-    handler: handlers.dataOTR,
-  },
-  {
-    topic: 'data.temperature',
-    aliases: ['Temperature'],
-    payloadSchema: { type: 'any' },
-    description: 'Push the current reactor temperature.',
-    handler: handlers.dataTemperature,
-  },
-  {
-    topic: 'data.dispersion',
-    aliases: ['Dispersion'],
-    payloadSchema: { type: 'any' },
-    description: 'Push a dispersion/mixing parameter update.',
-    handler: handlers.dataDispersion,
-  },
-  {
-    topic: 'child.register',
-    aliases: ['registerChild'],
-    payloadSchema: { type: 'any' },
-    description: 'Register a child node (settler / measurement) with this reactor.',
-    handler: handlers.childRegister,
-  },
-];

src/kinetics/baseEngine.js

@@ -1,139 +0,0 @@
-'use strict';
-
-const EventEmitter = require('events');
-const ASM3 = require('../reaction_modules/asm3_class.js');
-const { create, all } = require('mathjs');
-const { childRegistrationUtils, logger, MeasurementContainer, POSITIONS } = require('generalFunctions');
-
-const math = create(all, { matrix: 'Array' });
-
-const S_O_INDEX = 0;
-const NUM_SPECIES = 13;
-
-// Abstract reactor engine. Holds the influent/OTR/temperature state plus
-// the parent-side child registration that the original Reactor class
-// exposed. Concrete CSTR / PFR subclasses provide tick().
-class BaseReactorEngine {
-  constructor(config) {
-    this.config = config;
-    this.logger = new logger(
-      this.config.general.logging.enabled,
-      this.config.general.logging.logLevel,
-      config.general.name,
-    );
-    this.emitter = new EventEmitter();
-    this.measurements = new MeasurementContainer();
-    this.upstreamReactor = null;
-    this.childRegistrationUtils = new childRegistrationUtils(this);
-
-    this.asm = new ASM3();
-    this.volume = config.volume;
-
-    this.Fs = Array(config.n_inlets).fill(0);
-    this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0));
-    this.OTR = 0.0;
-    this.temperature = 20;
-
-    this.kla = config.kla;
-    this.currentTime = Date.now();
-    // timeStep stored in days (the integrator uses [d] internally).
-    this.timeStep = (1 / (24 * 60 * 60)) * this.config.timeStep;
-    this.speedUpFactor = config.speedUpFactor ?? 1;
-  }
-
-  set setInfluent(input) {
-    const index_in = input.payload.inlet;
-    this.Fs[index_in] = input.payload.F;
-    this.Cs_in[index_in] = input.payload.C;
-  }
-
-  set setOTR(input) { this.OTR = input.payload; }
-
-  set setTemperature(input) {
-    const p = input?.payload;
-    const raw = (p && typeof p === 'object' && p.value !== undefined) ? p.value : p;
-    const v = Number(raw);
-    if (!Number.isFinite(v)) { this.logger.warn(`Invalid temperature input: ${raw}`); return; }
-    this.temperature = v;
-  }
-
-  get getEffluent() {
-    const last = Array.isArray(this.state.at?.(-1)) ? this.state.at(-1) : this.state;
-    return { topic: 'Fluent', payload: { inlet: 0, F: math.sum(this.Fs), C: last }, timestamp: this.currentTime };
-  }
-
-  get getGridProfile() { return null; }
-
-  _calcOTR(S_O, T = 20.0) {
-    const sat = this._calcOxygenSaturation(T);
-    return this.kla * (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 sat = 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], sat));
-      return next;
-    };
-    return (Array.isArray(state) && Array.isArray(state[0])) ? state.map(capRow) : capRow(state);
-  }
-
-  _arrayClip2Zero(arr) {
-    if (Array.isArray(arr)) return arr.map((x) => this._arrayClip2Zero(x));
-    return arr < 0 ? 0 : arr;
-  }
-
-  registerChild(child, softwareType) {
-    switch (softwareType) {
-      case 'measurement': this._connectMeasurement(child); break;
-      case 'reactor':     this._connectReactor(child);     break;
-      default:            this.logger.error(`Unrecognized softwareType: ${softwareType}`);
-    }
-  }
-
-  _connectMeasurement(measurement) {
-    if (!measurement) { this.logger.warn('Invalid measurement provided.'); return; }
-    const fn = measurement.config.functionality;
-    const position = fn.distance !== 'undefined' ? fn.distance : fn.positionVsParent;
-    const measurementType = measurement.config.asset.type;
-    const eventName = `${measurementType}.measured.${position}`;
-    measurement.measurements.emitter.on(eventName, (eventData) => {
-      this.measurements
-        .type(measurementType).variant('measured').position(position)
-        .value(eventData.value, eventData.timestamp, eventData.unit);
-      this._updateMeasurement(measurementType, eventData.value, position, eventData);
-    });
-  }
-
-  _connectReactor(reactor) {
-    if (!reactor) { this.logger.warn('Invalid reactor provided.'); return; }
-    this.upstreamReactor = reactor;
-    reactor.emitter.on('stateChange', (data) => this.updateState(data));
-  }
-
-  _updateMeasurement(measurementType, value, position) {
-    if (measurementType === 'temperature' && position === POSITIONS.AT_EQUIPMENT) {
-      this.temperature = value;
-      return;
-    }
-    this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
-  }
-
-  updateState(newTime = Date.now()) {
-    const day2ms = 1000 * 60 * 60 * 24;
-    if (this.upstreamReactor) this.setInfluent = this.upstreamReactor.getEffluent;
-    const n_iter = Math.floor(this.speedUpFactor * (newTime - this.currentTime) / (this.timeStep * day2ms));
-    if (!n_iter) return;
-    for (let n = 0; n < n_iter; n += 1) this.tick(this.timeStep);
-    this.currentTime += (n_iter * this.timeStep * day2ms) / this.speedUpFactor;
-    this.emitter.emit('stateChange', this.currentTime);
-  }
-}
-
-module.exports = { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES };

src/kinetics/cstr.js

@@ -1,27 +0,0 @@
-'use strict';
-
-const { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES } = require('./baseEngine.js');
-
-class Reactor_CSTR extends BaseReactorEngine {
-  constructor(config) {
-    super(config);
-    this.state = config.initialState;
-  }
-
-  // Forward Euler step over `time_step` days.
-  tick(time_step) {
-    const inflow  = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
-    const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
-    const reaction = this.asm.compute_dC(this.state, this.temperature);
-    const transfer = Array(NUM_SPECIES).fill(0.0);
-    transfer[S_O_INDEX] = isNaN(this.kla)
-      ? this.OTR
-      : this._calcOTR(this.state[S_O_INDEX], this.temperature);
-
-    const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step);
-    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(math.add(this.state, dC_total)));
-    return this.state;
-  }
-}
-
-module.exports = Reactor_CSTR;

src/kinetics/pfr.js

@@ -1,132 +0,0 @@
-'use strict';
-
-const { assertNoNaN } = require('../utils.js');
-const { BaseReactorEngine, math, S_O_INDEX, NUM_SPECIES } = require('./baseEngine.js');
-
-class Reactor_PFR extends BaseReactorEngine {
-  constructor(config) {
-    super(config);
-
-    this.length = config.length;
-    this.n_x = config.resolution_L;
-    this.d_x = this.length / this.n_x;
-    this.A = this.volume / this.length;
-    this.alpha = config.alpha;
-
-    this.state = Array.from(Array(this.n_x), () => config.initialState.slice());
-    this.D = 0.0;
-
-    this.D_op  = this._makeDoperator(true, true);
-    this.D2_op = this._makeD2operator();
-    assertNoNaN(this.D_op,  'Derivative operator');
-    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,
-    };
-  }
-
-  set setDispersion(input) { this.D = input.payload; }
-
-  updateState(newTime) {
-    super.updateState(newTime);
-    const Pe_local = (this.d_x * math.sum(this.Fs)) / (this.D * this.A);
-    const Co_D = (this.D * this.timeStep) / (this.d_x * this.d_x);
-    if (Pe_local >= 2)  this.logger.warn(`Local Peclet number (${Pe_local}) is too high! Increase reactor resolution.`);
-    if (Co_D >= 0.5)    this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
-  }
-
-  // Explicit finite-difference step over `time_step` days.
-  tick(time_step) {
-    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((slice) => this.asm.compute_dC(slice, this.temperature));
-    const transfer   = Array.from(Array(this.n_x), () => new Array(NUM_SPECIES).fill(0));
-
-    const klaIsNaN = isNaN(this.kla);
-    for (let i = 1; i < this.n_x - 1; i += 1) {
-      const otr = klaIsNaN ? this.OTR : this._calcOTR(this.state[i][S_O_INDEX], this.temperature);
-      transfer[i][S_O_INDEX] = otr * this.n_x / (this.n_x - 2);
-    }
-
-    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer), time_step);
-    const stateNew = math.add(this.state, dC_total);
-    this._applyBoundaryConditions(stateNew);
-    this.state = this._capDissolvedOxygen(this._arrayClip2Zero(stateNew));
-    return stateNew;
-  }
-
-  _updateMeasurement(measurementType, value, position, context) {
-    if (measurementType === 'quantity (oxygen)') {
-      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}).`);
-        return;
-      }
-      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;
-      return;
-    }
-    super._updateMeasurement(measurementType, value, position, context);
-  }
-
-  // Generalised Danckwerts at inlet when flow > 0; Neumann (no-flux) at outlet
-  // and at inlet when there is no flow.
-  _applyBoundaryConditions(state) {
-    if (math.sum(this.Fs) > 0) {
-      const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
-      const BC_disp = ((1 - this.alpha) * this.D * this.A) / (math.sum(this.Fs) * this.d_x);
-      state[0] = math.multiply(1 / (1 + BC_disp), math.add(BC_C_in, math.multiply(BC_disp, state[1])));
-    } else {
-      state[0] = state[1];
-    }
-    state[this.n_x - 1] = state[this.n_x - 2];
-  }
-
-  _makeDoperator(central = false, higher_order = false) {
-    if (higher_order) {
-      if (!central) throw new Error('Upwind higher order method not implemented! Use central scheme instead.');
-      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);
-      // Preserve the pre-refactor aliasing: D[1] = NearBoundary; NearBoundary.reverse()
-      // mutates D[1] in place; then D[n_x-2] = -1 * NearBoundary uses the reversed view.
-      const nb = Array(this.n_x).fill(0.0);
-      nb[0] = -1 / 4; nb[1] = -5 / 6; nb[2] = 3 / 2; nb[3] = -1 / 2; nb[4] = 1 / 12;
-      D[1] = nb;
-      nb.reverse();
-      D[this.n_x - 2] = math.multiply(-1, nb);
-      D[0] = Array(this.n_x).fill(0);
-      D[this.n_x - 1] = Array(this.n_x).fill(0);
-      return D;
-    }
-    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);
-    D[this.n_x - 1] = Array(this.n_x).fill(0);
-    return D;
-  }
-
-  _makeD2operator() {
-    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);
-    D2[0] = Array(this.n_x).fill(0);
-    D2[this.n_x - 1] = Array(this.n_x).fill(0);
-    return D2;
-  }
-}
-
-module.exports = Reactor_PFR;

src/nodeClass.js

@@ -1,53 +1,165 @@
-'use strict';
+const { Reactor_CSTR, Reactor_PFR } = require('./specificClass.js');
 
-const { BaseNodeAdapter } = require('generalFunctions');
-const Reactor = require('./specificClass.js');
-const commands = require('./commands');
 
-const 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 {
+    /**
+    * Node-RED node class for advanced-reactor.
+    * @param {object} uiConfig - Node-RED node configuration
+    * @param {object} RED - Node-RED runtime API
+    * @param {object} nodeInstance - Node-RED node instance
+    * @param {string} nameOfNode - Name of the node
+    */
+    constructor(uiConfig, RED, nodeInstance, nameOfNode) {
+        // Preserve RED reference for HTTP endpoints if needed
+        this.node = nodeInstance;
+        this.RED = RED;
+        this.name = nameOfNode;
+        this.source = null;
 
-class nodeClass extends BaseNodeAdapter {
-  static DomainClass = Reactor;
-  static commands = commands;
-  // Tick-driven: ASM kinetics integrate over wall-clock time. The engine's
-  // updateState computes how many internal Euler/FD steps fit in the elapsed
-  // ms; without a periodic tick the integrator never advances.
-  static tickInterval = 1000;
-  static statusInterval = 1000;
+        this._loadConfig(uiConfig)
+        this._setupClass();
 
-  buildDomainConfig(uiConfig) {
-    const initialState = {};
-    for (const k of SPECIES) initialState[k] = parseFloat(uiConfig[`${k}_init`]);
-    return {
-      reactor: {
-        reactor_type: uiConfig.reactor_type,
-        volume:       parseFloat(uiConfig.volume),
-        length:       parseFloat(uiConfig.length),
-        resolution_L: parseInt(uiConfig.resolution_L, 10),
-        alpha:        parseFloat(uiConfig.alpha),
-        n_inlets:     parseInt(uiConfig.n_inlets, 10),
-        kla:          parseFloat(uiConfig.kla),
-        timeStep:     parseFloat(uiConfig.timeStep),
-        speedUpFactor: Number(uiConfig.speedUpFactor) || 1,
-      },
-      initialState,
-    };
-  }
+        this._attachInputHandler();
+        this._registerChild();
+        this._startTickLoop();
+        this._attachCloseHandler();
+    }
 
-  // The kinetics engine drives Port-0 effluent + grid-profile shapes that
-  // don't fit BaseNodeAdapter's delta-compressed payload. Override the
-  // periodic emission so the Fluent / GridProfile contract is preserved.
-  _emitOutputs() {
-    const src = this.source;
-    if (!src?.engine) return;
-    src.updateState(Date.now());
-    const grid = src.getGridProfile;
-    if (grid) this.node.send([{ topic: 'GridProfile', payload: grid }, null, null]);
-    const raw = src.getOutput();
-    const influx = this._output.formatMsg(raw, src.config || this.config, 'influxdb');
-    this.node.send([src.getEffluent, influx, null]);
-  }
+    /**
+     * Handle node-red input messages
+     */
+    _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);
+            }
+
+            if (done) {
+                done();
+            }
+        });
+    }
+
+    /**
+     * Parse node configuration
+     * @param {object} uiConfig Config set in UI in node-red
+     */
+    _loadConfig(uiConfig) {
+        this.config = {
+            general: {
+                name: uiConfig.name || this.name,
+                id: this.node.id,
+                unit: null,
+                logging: {
+                    enabled: uiConfig.enableLog,
+                    logLevel: uiConfig.logLevel
+                }
+            },
+            functionality: {
+                positionVsParent: uiConfig.positionVsParent || 'atEquipment', // Default to 'atEquipment' if not specified
+                softwareType: "reactor" // should be set in config manager
+            },
+            reactor_type: uiConfig.reactor_type,
+            volume: parseFloat(uiConfig.volume),
+            length: parseFloat(uiConfig.length),
+            resolution_L: parseInt(uiConfig.resolution_L),
+            alpha: parseFloat(uiConfig.alpha),
+            n_inlets: parseInt(uiConfig.n_inlets),
+            kla: parseFloat(uiConfig.kla),
+            initialState: [
+                parseFloat(uiConfig.S_O_init),
+                parseFloat(uiConfig.S_I_init),
+                parseFloat(uiConfig.S_S_init),
+                parseFloat(uiConfig.S_NH_init),
+                parseFloat(uiConfig.S_N2_init),
+                parseFloat(uiConfig.S_NO_init),
+                parseFloat(uiConfig.S_HCO_init),
+                parseFloat(uiConfig.X_I_init),
+                parseFloat(uiConfig.X_S_init),
+                parseFloat(uiConfig.X_H_init),
+                parseFloat(uiConfig.X_STO_init),
+                parseFloat(uiConfig.X_A_init),
+                parseFloat(uiConfig.X_TS_init)
+            ],
+            timeStep: parseFloat(uiConfig.timeStep)
+        }
+    }
+
+    /**
+     * Register this node as a child upstream and downstream.
+     * Delayed to avoid Node-RED startup race conditions.
+     */
+    _registerChild() {
+        setTimeout(() => {
+        this.node.send([
+            null,
+            null,
+            { topic: 'registerChild', payload: this.node.id, positionVsParent: this.config?.functionality?.positionVsParent || 'atEquipment' }
+        ]);
+        }, 100);
+    }
+
+    /**
+     * Setup reactor class based on config
+     */
+    _setupClass() {
+        let new_reactor;
+
+        switch (this.config.reactor_type) {
+            case "CSTR":
+                new_reactor = new Reactor_CSTR(this.config);
+                break;
+            case "PFR":
+                new_reactor = new Reactor_PFR(this.config);
+                break;
+            default:
+                console.warn("Unknown reactor type: " + uiConfig.reactor_type);
+        }
+
+        this.source = new_reactor; // protect from reassignment
+        this.node.source = this.source;
+    }
+
+    _startTickLoop() {
+        setTimeout(() => {
+            this._tickInterval = setInterval(() => this._tick(), 1000);
+        }, 1000);
+    }
+
+    _tick(){
+        this.node.send([this.source.getEffluent, null, null]);
+    }
+
+    _attachCloseHandler() {
+        this.node.on('close', (done) => {
+            clearInterval(this._tickInterval);
+            done();
+        });
+    }
 }
 
-module.exports = nodeClass;
+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_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
+    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 
@@ -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_S, S_NH, , S_NO, S_HCO, , X_S, X_H, X_STO, X_A] = state;
+    const [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = state;
     const { k_H, K_X, k_STO, nu_NO, K_O, K_NO, K_S, K_STO, mu_H_max, K_NH, K_HCO, b_H_O, b_H_NO, b_STO_O, b_STO_NO, mu_A_max, K_A_NH, K_A_O, K_A_HCO, b_A_O, b_A_NO } = this.kin_params;
     const { theta_H, theta_STO, theta_mu_H, theta_b_H_O, theta_b_H_NO, theta_b_STO_O, theta_b_STO_NO, theta_mu_A, theta_b_A_O, theta_b_A_NO } = this.temp_params;
 
@@ -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

@@ -1,134 +1,420 @@
-'use strict';
+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 EventEmitter = require('events');
 
-const { BaseDomain, statusBadge, POSITIONS } = require('generalFunctions');
-const Reactor_CSTR = require('./kinetics/cstr.js');
-const Reactor_PFR  = require('./kinetics/pfr.js');
+const mathConfig = {
+  matrix: 'Array' // use Array as the matrix type
+};
 
-const SPECIES_KEYS = ['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 math = create(all, mathConfig);
 
-// Reactor — biological reactor orchestrator (Unit-level). Wraps a CSTR or
-// PFR kinetics engine and exposes the BaseDomain surface to BaseNodeAdapter.
-// The engines own the ASM3 integration; this class wires child registration
-// through ChildRouter, holds the validated config, and presents getOutput /
-// getStatusBadge.
-class Reactor extends BaseDomain {
-  static name = 'reactor';
+const S_O_INDEX = 0;
+const NUM_SPECIES = 13;
+const BC_PADDING = 2;
+const DEBUG = false;
 
-  configure() {
-    const flat = this._flattenEngineConfig(this.config);
-    this.engine = this._buildEngine(flat);
+class Reactor {
+  /**
+   * Reactor base class.
+   * @param {object} config - Configuration object containing reactor parameters.
+   */
+  constructor(config) {
+    this.config = config;
+    // EVOLV stuff
+    this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name);
+    this.emitter = new EventEmitter();
+    this.measurements = new MeasurementContainer();
+    this.upstreamReactor = null;
+    this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
+    this.parent = []; // Gets assigned via child registration
 
-    // Re-emit upstream-reactor stateChange and engine stateChange events on
-    // the BaseDomain emitter so adapter listeners pick them up uniformly.
-    this.engine.emitter.on('stateChange', (t) => this.emitter.emit('stateChange', t));
+    this.upstreamReactor = null;
+    this.downstreamReactor = null;
 
-    // ChildRouter dispatches to engine handlers — keeps the existing
-    // _connectMeasurement / _connectReactor wiring intact, just centralised.
-    this.router.onRegister('measurement', (child) => this.engine._connectMeasurement(child));
-    this.router.onRegister('reactor',     (child) => this.engine._connectReactor(child));
+    this.asm = new ASM3();
 
-    // Bridge engine.measurements into the BaseDomain measurements container
-    // so getFlattenedOutput surfaces temperature / oxygen series.
-    this.measurements = this.engine.measurements;
+    this.volume = config.volume; // fluid volume reactor [m3]
+
+    this.Fs = Array(config.n_inlets).fill(0); // fluid debits per inlet [m3 d-1]
+    this.Cs_in = Array.from(Array(config.n_inlets), () => new Array(NUM_SPECIES).fill(0)); // composition influents
+    this.OTR = 0.0; // oxygen transfer rate [g O2 d-1 m-3]
+    this.temperature = 20; // temperature [C]
+
+    this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
+
+    this.currentTime = 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
   }
 
-  // Translate the nested schema config (reactor.*, initialState.*) into the
-  // flat shape the kinetics engines accept.
-  _flattenEngineConfig(config) {
-    const reactor = config.reactor || {};
-    const init = config.initialState || {};
-    const initialState = SPECIES_KEYS.map((k) => Number(init[k] ?? 0));
-    return {
-      general: config.general,
-      functionality: config.functionality,
-      reactor_type: reactor.reactor_type ?? 'CSTR',
-      volume: Number(reactor.volume),
-      length: Number(reactor.length),
-      resolution_L: Number(reactor.resolution_L),
-      alpha: Number(reactor.alpha),
-      n_inlets: Number(reactor.n_inlets),
-      kla: Number(reactor.kla),
-      timeStep: Number(reactor.timeStep),
-      speedUpFactor: Number(reactor.speedUpFactor) || 1,
-      initialState,
-    };
+  /**
+   * Setter for influent data.
+   * @param {object} input - Input object (msg) containing payload with inlet index, flow rate, and concentrations.
+  */
+  set setInfluent(input) {
+    let index_in = input.payload.inlet;
+    this.Fs[index_in] = input.payload.F;
+    this.Cs_in[index_in] = input.payload.C;
   }
 
-  _buildEngine(flat) {
-    // The schema enum validator lowercases the configured value, so accept
-    // either case.
-    switch (String(flat.reactor_type || '').toUpperCase()) {
-      case 'CSTR': return new Reactor_CSTR(flat);
-      case 'PFR':  return new Reactor_PFR(flat);
+  /**
+   * Setter for OTR (Oxygen Transfer Rate).
+   * @param {object} input - Input object (msg) containing payload with OTR value [g O2 d-1 m-3].
+   */
+  set setOTR(input) {
+    this.OTR = input.payload;
+  }
+
+  /**
+   * Getter for effluent data.
+   * @returns {object} Effluent data object (msg), defaults to inlet 0.
+   */
+  get getEffluent() { // getter for Effluent, defaults to inlet 0
+    if (isArray(this.state.at(-1))) {
+      return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state.at(-1) }, timestamp: this.currentTime };
+    }
+    return { topic: "Fluent", payload: { inlet: 0, F: math.sum(this.Fs), C: this.state }, timestamp: this.currentTime };
+  }
+
+  /**
+   * Calculate the oxygen transfer rate (OTR) based on the dissolved oxygen concentration and temperature.
+   * @param {number} S_O - Dissolved oxygen concentration [g O2 m-3].
+   * @param {number} T - Temperature in Celsius, default to 20 C.
+   * @returns {number} - Calculated OTR [g O2 d-1 m-3].
+   */
+  _calcOTR(S_O, T = 20.0) { // caculate the OTR using basic correlation, default to temperature: 20 C
+    let S_O_sat = 14.652 - 4.1022e-1 * T + 7.9910e-3 * T*T + 7.7774e-5 * T*T*T;
+    return this.kla * (S_O_sat - S_O);
+  }
+
+  /**
+   * Clip values in an array to zero.
+   * @param {Array} arr - Array of values to clip.
+   * @returns {Array} - New array with values clipped to zero.
+   */
+  _arrayClip2Zero(arr) {
+    if (Array.isArray(arr)) {
+      return arr.map(x => this._arrayClip2Zero(x));
+    } else {
+      return arr < 0 ? 0 : arr;
+    }
+  }
+
+  registerChild(child, softwareType) {
+    switch (softwareType) {
+      case "measurement":
+        this.logger.debug(`Registering measurement child.`);
+        this._connectMeasurement(child);
+        break;
+      case "reactor":
+        this.logger.debug(`Registering reactor child.`);
+        this._connectReactor(child);
+        break;
+
       default:
-        this.logger.warn(`Unknown reactor type: ${flat.reactor_type}. Falling back to CSTR.`);
-        return new Reactor_CSTR(flat);
+        this.logger.error(`Unrecognized softwareType: ${softwareType}`);
     }
   }
 
-  // Adapter input setters — forwarded straight to the engine.
-  set setInfluent(msg)    { this.engine.setInfluent = msg; }
-  set setOTR(msg)         { this.engine.setOTR = msg; }
-  set setTemperature(msg) { this.engine.setTemperature = msg; }
-  set setDispersion(msg)  { if (this.engine instanceof Reactor_PFR) this.engine.setDispersion = msg; }
-
-  updateState(t) { this.engine.updateState(t); this.notifyOutputChanged(); }
-
-  // Engine pass-through — needed so the BaseNodeAdapter tick loop (and
-  // tests calling reactor.tick(dt) directly) drive the ASM integration.
-  // Without this the Node-RED tick fires `source.tick?.()`, gets undefined,
-  // and the kinetics state never advances.
-  tick(timeStep) {
-    const result = this.engine.tick(timeStep);
-    this.notifyOutputChanged();
-    return result;
-  }
-
-  get getEffluent()    { return this.engine.getEffluent; }
-  get getGridProfile() { return this.engine.getGridProfile; }
-  get temperature()    { return this.engine.temperature; }
-
-  // Per-tick output for Port 0 / Port 1. Carries the effluent vector plus
-  // a flat per-species block keyed by SPECIES_KEYS for InfluxDB telemetry.
-  getOutput() {
-    const eff = this.engine.getEffluent;
-    const C = Array.isArray(eff?.payload?.C) ? eff.payload.C : [];
-    const out = {
-      flow_total: Number(eff?.payload?.F),
-      temperature: Number(this.engine.temperature),
-    };
-    for (let i = 0; i < Math.min(SPECIES_KEYS.length, C.length); i += 1) {
-      const v = Number(C[i]);
-      if (Number.isFinite(v)) out[SPECIES_KEYS[i]] = v;
+  _connectMeasurement(measurementChild) {
+    if (!measurementChild) {
+      this.logger.warn("Invalid measurement provided.");
+      return;
     }
-    return out;
+
+    const position = measurementChild.config.functionality.positionVsParent;
+    const measurementType = measurementChild.config.asset.type;
+    const eventName = `${measurementType}.measured.${position}`;
+
+    // Register event listener for measurement updates
+    measurementChild.measurements.emitter.on(eventName, (eventData) => {
+      this.logger.debug(`${position} ${measurementType} from ${eventData.childName}: ${eventData.value} ${eventData.unit}`);
+
+      // Store directly in parent's measurement container
+      this.measurements
+        .type(measurementType)
+        .variant("measured")
+        .position(position)
+        .value(eventData.value, eventData.timestamp, eventData.unit);
+      
+      this._updateMeasurement(measurementType, eventData.value, position, eventData);
+    });
   }
 
-  getStatusBadge() {
-    const eff = this.engine.getEffluent;
-    const F = Number(eff?.payload?.F) || 0;
-    const SO = Array.isArray(eff?.payload?.C) ? Number(eff.payload.C[0]) : NaN;
-    const so = Number.isFinite(SO) ? SO.toFixed(2) : '—';
-    return statusBadge.compose(
-      [`${this.engine.constructor.name.replace('Reactor_', '')}`,
-       `T=${Number(this.engine.temperature).toFixed(1)} C`,
-       `F=${F.toFixed(2)} m³/d`,
-       `S_O=${so} mg/L`],
-      { fill: 'green', shape: 'dot' },
-    );
+
+  _connectReactor(reactorChild) {
+    if (!reactorChild) {
+      this.logger.warn("Invalid reactor provided.");
+      return;
+    }
+
+    this.upstreamReactor = reactorChild;
+    reactorChild.downstreamReactor = this;
+
+    reactorChild.emitter.on("stateChange", (data) => {
+      this.logger.debug(`State change of upstream reactor detected.`);
+      this.updateState(data);
+    });
   }
 
-  close() {
-    this.engine?.emitter?.removeAllListeners?.();
-    super.close();
+  
+  _updateMeasurement(measurementType, value, position, context) {
+    this.logger.debug(`---------------------- updating ${measurementType} ------------------ `);
+    switch (measurementType) {
+      case "temperature":
+        if (position == "atEquipment") {
+          this.temperature = value;
+        }
+        break;
+      default:
+        this.logger.error(`Type '${measurementType}' not recognized for measured update.`);
+        return;
+    }
+  }
+
+  /**
+   * Update the reactor state based on the new time.
+   * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
+   */
+  updateState(newTime = Date.now()) { // expect update with timestamp
+    const day2ms = 1000 * 60 * 60 * 24;
+
+    if (this.upstreamReactor) {
+      this.setInfluent = this.upstreamReactor.getEffluent;
+    }
+
+    let n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*day2ms));
+    if (n_iter) {
+      let n = 0;
+      while (n < n_iter) {
+        this.tick(this.timeStep);
+        n += 1;
+      }
+      this.currentTime += n_iter * this.timeStep * day2ms / this.speedUpFactor;
+      this.emitter.emit("stateChange", this.currentTime);
+    }
   }
 }
 
-module.exports = Reactor;
-module.exports.Reactor = Reactor;
-module.exports.Reactor_CSTR = Reactor_CSTR;
-module.exports.Reactor_PFR  = Reactor_PFR;
-// POSITIONS is consumed by older test setups; surface it here so they don't
-// need to chase down generalFunctions internals.
-module.exports.POSITIONS    = POSITIONS;
+class Reactor_CSTR extends Reactor {
+  /**
+   * Reactor_CSTR class for Continuous Stirred Tank Reactor.
+   * @param {object} config - Configuration object containing reactor parameters.
+   */
+  constructor(config) {
+      super(config);
+      this.state = config.initialState;
+  }
+
+  /**
+   * Tick the reactor state using the forward Euler method.
+   * @param {number} time_step - Time step for the simulation [d].
+   * @returns {Array} - New reactor state.
+   */
+  tick(time_step) { // tick reactor state using forward Euler method
+    const inflow = math.multiply(math.divide([this.Fs], this.volume), this.Cs_in)[0];
+    const outflow = math.multiply(-1 * math.sum(this.Fs) / this.volume, this.state);
+    const reaction = this.asm.compute_dC(this.state, this.temperature);
+    const transfer = Array(NUM_SPECIES).fill(0.0);
+    transfer[S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
+
+    const dC_total = math.multiply(math.add(inflow, outflow, reaction, transfer), time_step)
+    this.state = this._arrayClip2Zero(math.add(this.state, dC_total)); // clip value element-wise to avoid negative concentrations
+    if(DEBUG){
+      assertNoNaN(dC_total, "change in state");
+      assertNoNaN(this.state, "new state");
+    }
+    return this.state;
+  }
+}
+
+class Reactor_PFR extends Reactor {
+  /**
+   * Reactor_PFR class for Plug Flow Reactor.
+   * @param {object} config - Configuration object containing reactor parameters.
+   */
+  constructor(config) {
+    super(config);
+
+    this.length = config.length; // reactor length [m]
+    this.n_x = config.resolution_L; // number of slices
+
+    this.d_x = this.length / this.n_x;
+    this.A = this.volume / this.length; // crosssectional area [m2]
+
+    this.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.D = 0.0; // axial dispersion [m2 d-1]
+
+    this.D_op = this._makeDoperator();
+    assertNoNaN(this.D_op, "Derivative operator");
+
+    this.D2_op = this._makeD2operator();
+    assertNoNaN(this.D2_op, "Second derivative operator");
+  }
+
+  /**
+   * Setter for axial dispersion.
+   * @param {object} input - Input object (msg) containing payload with dispersion value [m2 d-1].
+   */
+  set setDispersion(input) {
+    this.D = input.payload;
+  }
+
+  updateState(newTime) {
+    super.updateState(newTime);
+    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 (${Pe_local}) is too high! Increase reactor resolution.`);
+    (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
+
+    if(DEBUG) {
+      console.log("Inlet state max " + math.max(this.state[0]))
+      console.log("Pe total " + this.length*math.sum(this.Fs)/(this.D*this.A));
+      console.log("Pe local " + Pe_local);
+      console.log("Co ad " + math.sum(this.Fs)*this.timeStep/(this.A*this.d_x));
+      console.log("Co D " + Co_D);
+    }
+  }
+
+  /**
+   * Tick the reactor state using explicit finite difference method.
+   * @param {number} time_step - Time step for the simulation [d].
+   * @returns {Array} - New reactor state.
+   */
+  tick(time_step) {
+    this._applyBoundaryConditions();
+
+    const dispersion = math.multiply(this.D / (this.d_x*this.d_x), this.D2_op, this.extendedState);
+    const advection = math.multiply(-1 * math.sum(this.Fs) / (this.A*this.d_x), this.D_op, this.extendedState);
+    const reaction = this.extendedState.map((state_slice) => this.asm.compute_dC(state_slice, this.temperature));
+    const transfer = Array.from(Array(this.n_x+2*BC_PADDING), () => new Array(NUM_SPECIES).fill(0));
+
+    if (isNaN(this.kla)) { // calculate OTR if kla is not NaN, otherwise use externally calculated OTR
+      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+        transfer[i][S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
+      }
+    } 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);
+      }
+    }
+
+    const dC_total = math.multiply(math.add(dispersion, advection, reaction, transfer).slice(BC_PADDING, this.n_x+BC_PADDING), time_step);
+
+    const stateNew = math.add(this.state, dC_total);
+
+    if (DEBUG) {
+      assertNoNaN(dispersion, "dispersion");
+      assertNoNaN(advection, "advection");
+      assertNoNaN(reaction, "reaction");
+      assertNoNaN(dC_total, "change in state");
+      assertNoNaN(stateNew, "new state post BC");
+    }
+
+    this.state = this._arrayClip2Zero(stateNew);
+    this.state.forEach((row, i) => this.extendedState[i+BC_PADDING] = row);
+    return stateNew;
+  }
+
+  _updateMeasurement(measurementType, value, position, context) {
+    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
+        break;
+      default:
+        super._updateMeasurement(measurementType, value, position, context);
+    }
+  }
+
+  /**
+   * Apply boundary conditions to the reactor state.
+   *  for inlet, apply generalised Danckwerts BC, if there is not flow, apply Neumann BC with no flux
+   *  for outlet, apply regular Danckwerts BC (Neumann BC with no flux)
+   */
+  _applyBoundaryConditions() {
+    if (this.upstreamReactor) {
+      for (let i = 0; i < BC_PADDING; i++) {
+        this.extendedState[i] = this.upstreamReactor.state.at(i-BC_PADDING);
+      }
+    } else {
+      if (math.sum(this.Fs) > 0) { // Danckwerts BC
+        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);
+      }
+    }
+  }
+
+  /**
+   * Create finite difference first derivative operator.
+   * @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;
+  }
+
+  /**
+   * Create central finite difference second derivative operator.
+   * @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 D2 = math.add(I, A, B);
+    // set by BCs elsewhere
+    D2.forEach((row, i) => i < BC_PADDING || i >= this.n_x+BC_PADDING ? row.fill(0) : row);
+    return D2;
+  }
+}
+
+module.exports = { Reactor_CSTR, Reactor_PFR };
+
+// DEBUG
+// state: S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS
+// let initial_state = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1];
+// const Reactor = new Reactor_PFR(200, 10, 10, 1, 100, initial_state);
+// Reactor.Cs_in[0] = [0.0, 30., 100., 16., 0., 0., 5., 25., 75., 30., 0., 0., 125.];
+// Reactor.Fs[0] = 10;
+// Reactor.D = 0.01;
+// let N = 0;
+// while (N < 5000) {
+//     console.log(Reactor.tick(0.001));
+//     N += 1;
+// }

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

@@ -1,12 +0,0 @@
-# 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

@@ -1,83 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// The pre-refactor _loadConfig / _setupClass private methods are gone —
-// config build is exposed via buildDomainConfig (override hook in
-// CONTRACTS.md §2), and engine selection is observable via
-// `inst.source.engine instanceof Reactor_CSTR | Reactor_PFR` after a
-// full `new nodeClass(...)` construction.
-
-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 } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('buildDomainConfig coerces numeric fields and builds initial state vector', () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-  try {
-    const dc = inst.buildDomainConfig(
-      makeUiConfig({
-        volume: '12.5',
-        length: '9',
-        resolution_L: '7',
-        alpha: '0.5',
-        n_inlets: '3',
-        timeStep: '2',
-        S_O_init: '1.1',
-      }),
-    );
-
-    assert.equal(dc.reactor.volume, 12.5);
-    assert.equal(dc.reactor.length, 9);
-    assert.equal(dc.reactor.resolution_L, 7);
-    assert.equal(dc.reactor.alpha, 0.5);
-    assert.equal(dc.reactor.n_inlets, 3);
-    assert.equal(dc.reactor.timeStep, 2);
-    assert.equal(Object.keys(dc.initialState).length, 13);
-    assert.equal(dc.initialState.S_O, 1.1);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('Reactor wrapper instantiates CSTR engine when configured as CSTR', () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig({ reactor_type: 'CSTR' }), makeRED(), node, 'reactor');
-  try {
-    assert.ok(inst.source.engine instanceof Reactor_CSTR);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('Reactor wrapper instantiates PFR engine when configured as PFR', () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig({ reactor_type: 'PFR' }), makeRED(), node, 'reactor');
-  try {
-    assert.ok(inst.source.engine instanceof Reactor_PFR);
-  } finally {
-    closeNode(node);
-  }
-});

test/basic/cstr-tick.basic.test.js

@@ -1,42 +0,0 @@
-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

@@ -1,38 +0,0 @@
-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

@@ -1,45 +0,0 @@
-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

@@ -1,111 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// The pre-refactor _attachInputHandler private switch is gone — input
-// dispatch goes through the commands registry that BaseNodeAdapter builds
-// at construction. Tests fire msgs through `node.handlers.input` and
-// observe via `node.sends`, `inst.source.engine.*`, and per-fire calls
-// captured on a child stub registered through `RED.nodes.getNode(id)`.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeNode(id = 'reactor-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function makeRED(nodeMap = {}) {
-  return { nodes: { getNode: (id) => nodeMap[id] || null } };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('legacy alias topics drive engine setters and updateState', async () => {
-  const childSource = {
-    id: 'child-source-A',
-    config: { general: { id: 'child-source-A' }, functionality: { softwareType: 'measurement', positionVsParent: 'upstream' }, asset: { type: 'temperature' } },
-  };
-  const node = makeNode();
-  const RED = makeRED({ childA: { source: childSource } });
-  const inst = new nodeClass(makeUiConfig(), RED, node, 'reactor');
-
-  try {
-    let doneCount = 0;
-    const done = () => { doneCount += 1; };
-
-    // data.clock alias → updateState(timestamp). Capture currentTime
-    // before/after to verify the engine advanced.
-    const t0 = inst.source.engine.currentTime;
-    await node.handlers.input({ topic: 'clock', timestamp: t0 + 1 }, () => {}, done);
-
-    // Fluent alias → engine setInfluent setter.
-    await node.handlers.input(
-      { topic: 'Fluent', payload: { inlet: 0, F: 7, C: [1,2,3,4,5,6,7,8,9,10,11,12,13] } },
-      () => {}, done,
-    );
-    assert.equal(inst.source.engine.Fs[0], 7);
-    assert.deepEqual(inst.source.engine.Cs_in[0], [1,2,3,4,5,6,7,8,9,10,11,12,13]);
-
-    // OTR alias → engine setOTR setter.
-    await node.handlers.input({ topic: 'OTR', payload: 3.5 }, () => {}, done);
-    assert.equal(inst.source.engine.OTR, 3.5);
-
-    // Temperature alias → engine setTemperature setter.
-    await node.handlers.input({ topic: 'Temperature', payload: 18.2 }, () => {}, done);
-    assert.equal(inst.source.engine.temperature, 18.2);
-
-    // Dispersion alias — CSTR engine does not own a setDispersion setter
-    // (only PFR does); the Reactor wrapper guards on engine type and the
-    // dispatch should silently return without throwing.
-    await node.handlers.input({ topic: 'Dispersion', payload: 0.2 }, () => {}, done);
-
-    // registerChild alias → registers via childRegistrationUtils.
-    // The handler resolves the child via RED.nodes.getNode(payload).source.
-    await node.handlers.input(
-      { topic: 'registerChild', payload: 'childA', positionVsParent: 'upstream' },
-      () => {}, done,
-    );
-
-    assert.equal(doneCount, 6);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('canonical topics are accepted (data.fluent, data.otr, data.temperature)', async () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let done = 0;
-    await node.handlers.input(
-      { topic: 'data.fluent', payload: { inlet: 0, F: 11, C: [0,0,0,0,0,0,0,0,0,0,0,0,0] } },
-      () => {}, () => { done += 1; },
-    );
-    assert.equal(inst.source.engine.Fs[0], 11);
-
-    await node.handlers.input({ topic: 'data.otr', payload: 4.2 }, () => {}, () => { done += 1; });
-    assert.equal(inst.source.engine.OTR, 4.2);
-
-    await node.handlers.input({ topic: 'data.temperature', payload: 19.7 }, () => {}, () => { done += 1; });
-    assert.equal(inst.source.engine.temperature, 19.7);
-
-    assert.equal(done, 3);
-  } finally {
-    closeNode(node);
-  }
-});

test/basic/pfr-operators.basic.test.js

@@ -1,27 +0,0 @@
-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

@@ -1,84 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// The pre-refactor _registerChild method was renamed to
-// _scheduleRegistration inside BaseNodeAdapter and now fires automatically
-// 100ms after construction. We verify the emission by capturing the Port-2
-// message on `node.sends` after the registration delay elapses.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('scheduled child.register message lands on Port 2 after construction', async () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ positionVsParent: 'downstream' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-
-  try {
-    // BaseNodeAdapter._scheduleRegistration uses a 100ms setTimeout; wait
-    // slightly longer to let it fire.
-    await new Promise((r) => setTimeout(r, 130));
-
-    // The registration send is the [null, null, {child.register}] triple.
-    const regSends = node.sends.filter(
-      (s) => Array.isArray(s) && s[0] === null && s[1] === null && s[2] && s[2].topic === 'child.register',
-    );
-    assert.equal(regSends.length, 1, 'exactly one child.register message expected');
-    const msg = regSends[0][2];
-    assert.equal(msg.topic, 'child.register');
-    assert.equal(msg.payload, node.id);
-    assert.equal(msg.positionVsParent, 'downstream');
-    // After construction the source is exposed on the node for sibling lookup.
-    assert.strictEqual(node.source, inst.source);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('child.register handler ignores unknown child ids without throwing', async () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let done = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { topic: 'child.register', payload: 'missing-child', positionVsParent: 'upstream' },
-        () => {},
-        () => { done += 1; },
-      );
-    });
-    assert.equal(done, 1);
-    // No child should have been registered into the engine's registry.
-    const registered = inst.source.engine.childRegistrationUtils;
-    assert.ok(registered, 'childRegistrationUtils exists on engine');
-  } finally {
-    closeNode(node);
-  }
-});

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

@@ -1,91 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface for
-// the nodeClass-level checks, and the public Reactor_CSTR engine surface
-// for the domain-level checks. The pre-refactor private nodeClass methods
-// are gone — `buildDomainConfig` is the documented override hook
-// (CONTRACTS.md §2) and is fair game to call on a real constructed
-// instance.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeReactorConfig, makeUiConfig } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('Reactor_CSTR engine 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('Reactor_CSTR engine 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('Reactor_CSTR engine 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('buildDomainConfig propagates speedUpFactor from uiConfig', () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-  try {
-    const dc = inst.buildDomainConfig(makeUiConfig({ speedUpFactor: 5 }));
-    assert.equal(dc.reactor.speedUpFactor, 5);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('buildDomainConfig defaults speedUpFactor to 1 when missing from uiConfig', () => {
-  const node = makeNode();
-  const inst = new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-  try {
-    const ui = makeUiConfig();
-    delete ui.speedUpFactor;
-    const dc = inst.buildDomainConfig(ui);
-    assert.equal(dc.reactor.speedUpFactor, 1);
-  } finally {
-    closeNode(node);
-  }
-});
-
-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);
-
-  const t0 = reactor.currentTime;
-  reactor.updateState(t0 + 2000);
-
-  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

@@ -1,8 +0,0 @@
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-test('reactor module load smoke', () => {
-  assert.doesNotThrow(() => {
-    require('../../reactor.js');
-  });
-});

test/basic/timestep-units.basic.test.js

@@ -1,44 +0,0 @@
-'use strict';
-
-// Locks in the contract that `config.timeStep` is interpreted as SECONDS by
-// the reactor kinetics engine. Before 2026-05-19 the schema labelled the field
-// `unit: "h"` while reactor.html labelled it `[s]` and baseEngine divided by
-// 86400 (seconds-per-day) to convert to internal days. A 0.001 schema default
-// — read as hours — would have produced a 3.6 s step; read as seconds it is a
-// 1 ms step. The fix aligned the schema to seconds. This test prevents the
-// drift from reappearing.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeReactorConfig } = require('../helpers/factories');
-
-const SECONDS_PER_DAY = 24 * 60 * 60;
-
-function makeEngine(timeStepSeconds) {
-  return new Reactor_CSTR(makeReactorConfig({ reactor_type: 'CSTR', n_inlets: 1, timeStep: timeStepSeconds }));
-}
-
-test('engine stores timeStep in days, treating input as seconds', () => {
-  const eng = makeEngine(1);
-  assert.ok(Math.abs(eng.timeStep - 1 / SECONDS_PER_DAY) < 1e-15,
-    `engine.timeStep should be 1/86400 days for a 1-second config; got ${eng.timeStep}`);
-});
-
-test('engine timeStep scales linearly with config.timeStep (seconds in)', () => {
-  const a = makeEngine(1);
-  const b = makeEngine(10);
-  assert.ok(Math.abs(b.timeStep - 10 * a.timeStep) < 1e-15,
-    'engine.timeStep must scale linearly with config.timeStep; broke the seconds→days conversion');
-});
-
-test('schema default for timeStep matches the seconds convention', () => {
-  const path = require('node:path');
-  const gfRoot = path.dirname(require.resolve('generalFunctions'));
-  const schema = require(path.join(gfRoot, 'src/configs/reactor.json'));
-  assert.equal(schema.reactor.timeStep.rules.unit, 's',
-    'schema timeStep.unit must be "s" — engine treats input as seconds');
-  assert.equal(schema.reactor.timeStep.default, 1,
-    'schema timeStep.default must be 1 (1 second), matching reactor.html');
-});

test/edge/invalid-reactor-type.edge.test.js

@@ -1,65 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// The schema validator coerces `reactor_type` through the enum — values
-// outside `CSTR` / `PFR` are remapped to the default `CSTR` at validation
-// time. The Reactor wrapper additionally falls back to CSTR if anything
-// unrecognised slips through (defensive guard). Either way, the observable
-// effect after `new nodeClass(...)` is `inst.source.engine instanceof
-// Reactor_CSTR`.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { Reactor_CSTR } = require('../../src/specificClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('Reactor wrapper falls back to CSTR when reactor_type is unknown', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: 'UNKNOWN_TYPE' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-  try {
-    assert.ok(inst.source.engine instanceof Reactor_CSTR);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('Reactor wrapper falls back to CSTR when reactor_type is empty string', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: '' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-  try {
-    assert.ok(inst.source.engine instanceof Reactor_CSTR);
-  } finally {
-    closeNode(node);
-  }
-});

test/edge/invalid-topic.edge.test.js

@@ -1,68 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface. The
-// commands registry built by BaseNodeAdapter logs a warn on unknown topics
-// and still calls done — no throw.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('unknown input topic does not throw and still calls done', async () => {
-  const node = makeNode();
-  new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let doneCalled = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { topic: 'somethingUnknown', payload: 1 },
-        () => {},
-        () => { doneCalled += 1; },
-      );
-    });
-    assert.equal(doneCalled, 1);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('missing topic field is handled gracefully', async () => {
-  const node = makeNode();
-  new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let doneCalled = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { payload: 'no-topic-here' },
-        () => {},
-        () => { doneCalled += 1; },
-      );
-    });
-    assert.equal(doneCalled, 1);
-  } finally {
-    closeNode(node);
-  }
-});

test/edge/missing-child.edge.test.js

@@ -1,91 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// A child.register / registerChild msg with an unknown id should resolve
-// to no-op (the handler logs warn, no throw) and still call done.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeRED(nodeMap = {}) {
-  return { nodes: { getNode: (id) => nodeMap[id] || null } };
-}
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-test('registerChild alias with unknown id is ignored without throwing', async () => {
-  const node = makeNode();
-  new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let done = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { topic: 'registerChild', payload: 'missing-child', positionVsParent: 'upstream' },
-        () => {},
-        () => { done += 1; },
-      );
-    });
-    assert.equal(done, 1);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('child.register canonical topic with unknown id is ignored without throwing', async () => {
-  const node = makeNode();
-  new nodeClass(makeUiConfig(), makeRED(), node, 'reactor');
-
-  try {
-    let done = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { topic: 'child.register', payload: 'missing-child', positionVsParent: 'upstream' },
-        () => {},
-        () => { done += 1; },
-      );
-    });
-    assert.equal(done, 1);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('child.register with a child that has no .source is ignored without throwing', async () => {
-  const node = makeNode();
-  // The looked-up RED node exists but lacks a `.source` — the handler
-  // guards against this and logs warn.
-  new nodeClass(makeUiConfig(), makeRED({ orphan: {} }), node, 'reactor');
-
-  try {
-    let done = 0;
-    await assert.doesNotReject(async () => {
-      await node.handlers.input(
-        { topic: 'child.register', payload: 'orphan', positionVsParent: 'upstream' },
-        () => {},
-        () => { done += 1; },
-      );
-    });
-    assert.equal(done, 1);
-  } finally {
-    closeNode(node);
-  }
-});

test/edge/pfr-measurement-grid.edge.test.js

@@ -1,16 +0,0 @@
-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

@@ -1,11 +0,0 @@
-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

@@ -1,27 +0,0 @@
-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

@@ -1,149 +0,0 @@
-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: 200,
-    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

@@ -1,26 +0,0 @@
-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

@@ -1,91 +0,0 @@
-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

@@ -1,35 +0,0 @@
-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

@@ -1,23 +0,0 @@
-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

@@ -1,156 +0,0 @@
-'use strict';
-
-// Phase 10 rewrite: drives only the public BaseNodeAdapter surface.
-// The pre-refactor _tick / _startTickLoop methods are gone — periodic
-// emission lives in `_emitOutputs()` (overridden in the reactor nodeClass
-// to preserve the Fluent / GridProfile Port-0 contract; delta-compressed
-// payloads can't carry the C-vector). The override is part of the
-// documented BaseNodeAdapter override surface, so we exercise it
-// directly. The fully-constructed adapter wires `inst.source.engine`,
-// `inst._output`, etc. so we don't have to assemble stub bags.
-
-const test = require('node:test');
-const assert = require('node:assert/strict');
-
-const nodeClass = require('../../src/nodeClass');
-const { makeUiConfig } = require('../helpers/factories');
-
-function makeRED() { return { nodes: { getNode: () => null } }; }
-
-function makeNode(id = 'reactor-node-1') {
-  const sends = [];
-  const statuses = [];
-  const handlers = {};
-  return {
-    id, sends, statuses, handlers,
-    send(arr)  { sends.push(arr); },
-    status(b)  { statuses.push(b); },
-    on(ev, fn) { handlers[ev] = fn; },
-    warn() {}, error() {},
-  };
-}
-
-function closeNode(node) {
-  if (node.handlers.close) node.handlers.close(() => {});
-}
-
-function pickEffluentSends(node) {
-  return node.sends.filter((s) => Array.isArray(s) && s[0] && s[0].topic === 'Fluent');
-}
-
-function pickGridSends(node) {
-  return node.sends.filter((s) => Array.isArray(s) && s[0] && s[0].topic === 'GridProfile');
-}
-
-test('_emitOutputs sends the effluent message on process output (CSTR)', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: 'CSTR' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-
-  try {
-    // Reset sends so any construction-time emissions don't pollute the
-    // assertion (the registration triple lands on the same buffer).
-    node.sends.length = 0;
-    inst._emitOutputs();
-
-    const fluentSends = pickEffluentSends(node);
-    assert.equal(fluentSends.length, 1, 'exactly one Fluent message');
-    const triple = fluentSends[0];
-    assert.equal(triple[0].topic, 'Fluent');
-    assert.ok(triple[0].payload && Array.isArray(triple[0].payload.C));
-    // CSTR has no grid profile.
-    assert.equal(pickGridSends(node).length, 0);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('_emitOutputs emits a GridProfile message when engine exposes one (PFR)', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: 'PFR' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-
-  try {
-    node.sends.length = 0;
-    inst._emitOutputs();
-
-    assert.equal(pickGridSends(node).length, 1, 'exactly one GridProfile message');
-    assert.equal(pickEffluentSends(node).length, 1, 'exactly one Fluent message');
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('_emitOutputs formats per-species influx telemetry via outputUtils', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: 'CSTR' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-
-  try {
-    // Stub updateState so the engine integration does not overwrite the
-    // engineered state we want the telemetry formatter to see.
-    inst.source.updateState = () => {};
-    inst.source.engine.setInfluent = {
-      payload: { inlet: 0, F: 42, C: [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500] },
-    };
-    inst.source.engine.state = [2.1, 30, 100, 16, 0, 1, 8, 25, 75, 1500, 0, 15, 2500];
-    inst.source.engine.temperature = 19.5;
-
-    let captured = null;
-    const realFormat = inst._output.formatMsg.bind(inst._output);
-    inst._output.formatMsg = (output, cfg, format) => {
-      if (format === 'influxdb') captured = { output, format };
-      return realFormat(output, cfg, format);
-    };
-
-    node.sends.length = 0;
-    inst._emitOutputs();
-
-    assert.ok(captured, 'formatMsg was called with influxdb format');
-    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);
-  } finally {
-    closeNode(node);
-  }
-});
-
-test('Reactor.tick(dt) drives the kinetics engine and advances state', () => {
-  const node = makeNode();
-  const inst = new nodeClass(
-    makeUiConfig({ reactor_type: 'CSTR' }),
-    makeRED(),
-    node,
-    'reactor',
-  );
-
-  try {
-    // Feed an influent so the integrator has something to chew on.
-    inst.source.engine.setInfluent = {
-      payload: { inlet: 0, F: 5, C: [0,30,100,16,0,0,5,25,75,30,0,0.001,125] },
-    };
-
-    const stateBefore = JSON.stringify(inst.source.engine.state);
-    inst.source.tick(0.001);
-    const stateAfter = JSON.stringify(inst.source.engine.state);
-
-    assert.notEqual(stateBefore, stateAfter, 'engine state should advance after tick(dt)');
-  } finally {
-    closeNode(node);
-  }
-});

test/integration/upstream-reactor.integration.test.js

@@ -1,48 +0,0 @@
-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

@@ -1,346 +0,0 @@
-/**
- * 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);
-    });
-  });
-});

wiki/Home.md

@@ -1,182 +0,0 @@
-# reactor
-
-![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue) ![s88](https://img.shields.io/badge/S88-Unit-50a8d9) ![status](https://img.shields.io/badge/status-pending--review-orange)
-
-A `reactor` models a single biological-treatment tank governed by the ASM3 (Activated Sludge Model No. 3) kinetics. It wraps either a CSTR (fully-mixed) or PFR (plug-flow with axial dispersion) integrator, accepts an influent stream + aeration rate, integrates the 13 ASM3 species each tick, and emits the effluent vector for the next Unit downstream (typically a `settler` or another `reactor`). A `diffuser` (Equipment Module) supplies aeration via `data.otr`; `measurement` children supply temperature and (PFR-only) dissolved-oxygen reconciliation.
-
-> [!NOTE]
-> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
-
----
-
-## At a glance
-
-| Thing | Value |
-|:---|:---|
-| What it represents | One biological-treatment tank running ASM3 kinetics — aerated, anoxic, or anaerobic |
-| S88 level | Unit |
-| Use it when | You need an activated-sludge tank with nitrification / denitrification / heterotrophic growth modelled species-by-species |
-| Don't use it for | Passive equalisation tanks (no reactions), simple residence-time delays (lighter buffer is better), aerobic-only contactors where ASM3's full 13-species vector is overkill |
-| Children it accepts | `measurement` (temperature at equipment; PFR also: dissolved oxygen at numeric distance); upstream `reactor` |
-| Parents / sinks it talks to | downstream `reactor` or `settler` (via `Fluent` on Port 0); `diffuser` pushes `data.otr` in |
-
----
-
-## How it fits
-
-```mermaid
-flowchart LR
-    upstream[reactor<br/>upstream<br/>Unit]:::unit
-    rx[reactor<br/>Unit]:::unit
-    settler[settler<br/>downstream<br/>Unit]:::unit
-    diffuser[diffuser<br/>Equipment]:::equip
-    tsens[measurement<br/>temperature<br/>atEquipment]:::ctrl
-    osens[measurement<br/>quantity (oxygen)<br/>at numeric distance, PFR only]:::ctrl
-
-    upstream -.stateChange.-> rx
-    rx -->|Fluent inlet=0| settler
-    diffuser -->|data.otr| rx
-    tsens -.measured.-> rx
-    osens -.measured.-> rx
-    tsens -->|child.register| rx
-    osens -->|child.register| rx
-    upstream -->|child.register<br/>positionVsParent=upstream| rx
-
-    classDef unit fill:#50a8d9,color:#000
-    classDef equip fill:#86bbdd,color:#000
-    classDef ctrl fill:#a9daee,color:#000
-```
-
-S88 colours are anchored in `.claude/rules/node-red-flow-layout.md`.
-
-reactor sits on lane **L4** (Unit). The `diffuser` (lane L3) is **not** a registered child &mdash; it just pushes aeration via the `data.otr` topic. A reactor chain (multi-stage treatment, e.g. anoxic &rarr; aerobic &rarr; aerobic) is built by registering each upstream reactor with `positionVsParent: 'upstream'`; downstream reactors then `getEffluent` from the upstream on every `stateChange`.
-
----
-
-## Try it &mdash; 3-minute demo
-
-Import the basic example flow, deploy, and watch a CSTR consume influent over the simulation clock.
-
-```bash
-curl -X POST -H 'Content-Type: application/json' \
-  --data @nodes/reactor/examples/basic.flow.json \
-  http://localhost:1880/flow
-```
-
-What to click after deploy (each inject maps one-to-one to a topic in [Reference &mdash; Contracts](Reference-Contracts#topic-contract)):
-
-1. `data.fluent` &mdash; inject an influent stream `{inlet: 0, F: 1000, C: [...13 species...]}` (m³/d, mg/L). The 13 species follow ASM3 ordering.
-2. `data.temperature` &mdash; set reactor temperature (default 20 &deg;C; nitrification rates depend on this).
-3. `data.otr` (if `kla` is `NaN`) **or** rely on the configured `kla` for internal aeration.
-4. `data.clock` &mdash; push wall-clock `msg.timestamp` to advance the integrator. The engine computes `n_iter = floor(speedUpFactor &times; &Delta;t_wall / timeStep_days)` internal Euler / FD steps and integrates them in one shot.
-5. Watch Port 0 (`Fluent` envelope on every advance) and Port 1 (InfluxDB scalar fields: `flow_total`, `temperature`, `S_O`&hellip;`X_TS`).
-
-> [!IMPORTANT]
-> **GIF needed.** Demo recording of steps 1&ndash;5 with `S_NH` falling and `S_NO` rising (nitrification proceeding). Save as `wiki/_partial-gifs/reactor/01-basic-cstr.gif`, target &le; 1&nbsp;MB after `gifsicle -O3 --lossy=80`.
-
----
-
-## The six things you'll send
-
-| Topic | Aliases | Payload | What it does |
-|:---|:---|:---|:---|
-| `data.clock` | `clock` | `{timestamp: ms}` (or use `msg.timestamp`) | Advance the integrator. `updateState` computes how many internal steps fit between `currentTime` and the supplied timestamp (scaled by `speedUpFactor`) and runs them. |
-| `data.fluent` | `Fluent` | `{inlet: number, F: number, C: number[13]}` | Set the per-inlet flow rate (`F`) and concentration vector (`C`). Stored in `engine.Fs[inlet]` / `engine.Cs_in[inlet]`. |
-| `data.otr` | `OTR` | numeric | Set the externally-supplied oxygen transfer rate. Used when `kla` is `NaN`; ignored otherwise (internal mass transfer takes over). |
-| `data.temperature` | `Temperature` | numeric or `{value: number}` | Set `engine.temperature` (&deg;C). Non-numeric payloads are warned and ignored. |
-| `data.dispersion` | `Dispersion` | numeric | **PFR only** &mdash; set axial dispersion coefficient `D` (m²/d). Triggers Peclet / Courant guard warnings on the next `updateState`. |
-| `child.register` | `registerChild` | child node id (string) | Register a sibling node (`measurement`, upstream `reactor`) with this reactor. Port 2 wiring does this automatically in normal flows. |
-
-> [!NOTE]
-> Pending full node review (2026-05). reactor's command surface is data-push only &mdash; there is **no FSM, no setpoint, no mode**. The kinetics engine runs continuous-state ODE / PDE integration; the only stateful event is `stateChange` after every successful advance.
-
----
-
-## What you'll see come out
-
-Sample Port 0 message (CSTR mid-integration, nitrifying):
-
-```json
-{
-  "topic": "Fluent",
-  "payload": {
-    "inlet": 0,
-    "F": 1000,
-    "C": [2.1, 30, 12.4, 0.8, 4.3, 18.6, 4.2, 1050, 65, 2150, 4.5, 215, 3680]
-  },
-  "timestamp": 1747500000000
-}
-```
-
-The `C` array is the 13-species ASM3 vector in fixed order (indices 0&ndash;6 soluble, 7&ndash;12 particulate). For a PFR an additional message goes out on the same port **before** the effluent each advance:
-
-```json
-{
-  "topic": "GridProfile",
-  "payload": {
-    "grid": [[...13...], [...13...], "...n_x rows..."],
-    "n_x": 10,
-    "d_x": 1.0,
-    "length": 10,
-    "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": 1747500000000
-  }
-}
-```
-
-Port 1 (InfluxDB telemetry) carries the same data flattened as scalar fields &mdash; `flow_total` (m³/d), `temperature` (&deg;C), and one field per 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`, mg/L; `S_HCO` is mmol/L).
-
-| Field | Meaning |
-|:---|:---|
-| `S_O` | Dissolved oxygen. Capped to saturation at each tick via `_capDissolvedOxygen`. |
-| `S_I` | Inert soluble COD. |
-| `S_S` | Readily biodegradable substrate. |
-| `S_NH` | Ammonium nitrogen. Drops during nitrification. |
-| `S_N2` | Dinitrogen (denitrification end product). |
-| `S_NO` | Nitrate / nitrite nitrogen. Rises during nitrification. |
-| `S_HCO` | Alkalinity (bicarbonate, mmol/L). |
-| `X_I` | Inert particulate COD. |
-| `X_S` | Slowly biodegradable substrate. |
-| `X_H` | Heterotrophic biomass. |
-| `X_STO` | Stored COD in biomass. |
-| `X_A` | Autotrophic biomass. **Must be &ge; ~50 mg/L for nitrification to proceed.** |
-| `X_TS` | Total suspended solids. Drives the downstream settler split. |
-| `flow_total` | Effluent volumetric flow (m³/d) &mdash; `sum(Fs)`. |
-| `temperature` | Reactor temperature (&deg;C). |
-
----
-
-## The interesting bits
-
-### CSTR vs PFR
-
-The engine is selected once at `configure()` from `reactor.reactor_type`. The same input topics drive both, but PFR additionally:
-
-- Discretises the tank along the `length` axis into `resolution_L` grid cells (`n_x`).
-- Emits a `GridProfile` message **before** the effluent each `updateState`.
-- Honours `data.dispersion` to set the axial dispersion coefficient.
-- Reconciles oxygen measurements at a **numeric** `positionVsParent` (interpreted as distance from inlet) into the nearest grid cell.
-- Warns when local Peclet &ge; 2 or Courant &ge; 0.5 (stability of the explicit FD scheme).
-
-Hot-swapping engine type at runtime is not supported &mdash; redeploy the flow.
-
-### Aeration: internal `kla` vs external `data.otr`
-
-`reactor.kla > 0` enables internal mass-transfer: `OTR = kla &times; (sat(T) &minus; S_O)`. Set `kla = NaN` to fall through to the externally-pushed `data.otr` value (the path a `diffuser` Equipment node uses).
-
-### `X_A` footgun
-
-The HTML editor form's default initial autotroph biomass is `0.001` mg/L &mdash; effectively zero, so nitrification never starts. The JSON schema default is `200` mg/L. Always check the deployed node's form value before expecting `S_NH` to drop. See [Reference &mdash; Limitations](Reference-Limitations#x_a-initial-default-footgun).
-
----
-
-## Need more?
-
-| Page | What you'll find |
-|:---|:---|
-| [Reference &mdash; Contracts](Reference-Contracts) | Full topic contract, config schema, child registration filters |
-| [Reference &mdash; Architecture](Reference-Architecture) | Code map, integration sequence, kinetics layout, output ports |
-| [Reference &mdash; Examples](Reference-Examples) | Shipped example flows + debug recipes |
-| [Reference &mdash; Limitations](Reference-Limitations) | When not to use, known limitations, open questions |
-
-[EVOLV master wiki](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Home) &middot; [Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns) &middot; [Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions)

wiki/Reference-Architecture.md

@@ -1,293 +0,0 @@
-# Reference — Architecture
-
-![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
-
-> [!NOTE]
-> Code structure for `reactor`: the three-tier sandwich, the `src/` layout, the ASM3 kinetics engines (CSTR + PFR), the integration sequence, child registration, and the output-port pipeline. For an intuitive overview, return to [Home](Home).
->
-> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
-
----
-
-## Three-tier code layout
-
-```
-nodes/reactor/
-|
-+-- reactor.js                     entry: RED.nodes.registerType('reactor', NodeClass)
-|
-+-- src/
-|     nodeClass.js                 extends BaseNodeAdapter (Node-RED bridge)
-|     specificClass.js             extends BaseDomain (orchestration only)
-|     utils.js                     assertNoNaN + small helpers
-|     |
-|     +-- commands/
-|     |     index.js               6 topic descriptors
-|     |     handlers.js            pure handler functions
-|     |
-|     +-- kinetics/
-|     |     baseEngine.js          BaseReactorEngine (influent / OTR / T / child wiring / updateState)
-|     |     cstr.js                Reactor_CSTR extends BaseReactorEngine (0-D Forward Euler)
-|     |     pfr.js                 Reactor_PFR  extends BaseReactorEngine (axial FD + Danckwerts BC)
-|     |
-|     +-- reaction_modules/
-|     |     asm3_class.js          ASM3 stoichiometry + rate vector + species list
-|     |     asm3_class Koch.js     legacy variant (not consumed by current engines)
-|     |
-|     +-- io/                      reserved (currently empty)
-|
-+-- additional_nodes/
-|     recirculation-pump.{js,html} legacy companion node shipped from this repo
-|     settling-basin.{js,html}     legacy companion node shipped from this repo
-```
-
-### Tier responsibilities
-
-| Tier | File | What it owns | Touches `RED.*` |
-|:---|:---|:---|:---:|
-| entry | `reactor.js` | Type registration | Yes |
-| nodeClass | `src/nodeClass.js` | Tick loop (`tickInterval = 1000` ms), status badge (`statusInterval = 1000` ms), `buildDomainConfig` mapping editor fields to nested config, `_emitOutputs` override that preserves the `Fluent` + `GridProfile` envelope (BaseNodeAdapter's default delta-compressed payload doesn't fit). | Yes |
-| specificClass | `src/specificClass.js` | `_flattenEngineConfig` translates nested schema to engine shape; `_buildEngine` selects CSTR or PFR; wires ChildRouter (`measurement` → `engine._connectMeasurement`, `reactor` → `engine._connectReactor`); re-emits engine `stateChange` on the BaseDomain emitter; surfaces `getOutput()`, `getStatusBadge()`. | No |
-| kinetics | `src/kinetics/*.js` | Pure ASM3 integration. `BaseReactorEngine` owns influent state, OTR, temperature, child-registration utils, and `updateState`. `Reactor_CSTR` adds the 0-D Forward-Euler tick. `Reactor_PFR` adds spatial discretization + boundary conditions + grid-profile emission. | No |
-
-`specificClass` is thin stitching. All the real work lives in the kinetics engines.
-
----
-
-## No FSM — continuous-state integration
-
-reactor has **no finite-state machine, no mode, no setpoint**. The engine runs continuous ODE / PDE integration in process time. The only stateful event is `stateChange`, emitted by `BaseReactorEngine.updateState` after every successful advance (`n_iter > 0` internal steps completed).
-
-```mermaid
-flowchart LR
-    clk[data.clock<br/>or tick&#40;dt&#41;]:::input --> us[updateState&#40;newTime&#41;]
-    us --> ni{n_iter = floor&#40;<br/>speedUpFactor &times; &Delta;t / timeStep&#41;}
-    ni -->|0| skip[no-op]
-    ni -->|>0| loop[for each step:<br/>tick&#40;timeStep&#41;]
-    loop --> emit[emit stateChange&#40;currentTime&#41;]
-    classDef input fill:#a9daee,color:#000
-```
-
-`stateChange` is the trigger downstream Units (settlers, chained reactors) use to pull effluent.
-
----
-
-## Kinetics engines &mdash; CSTR vs PFR
-
-```mermaid
-flowchart TB
-    subgraph base["BaseReactorEngine"]
-        bs["Fs[], Cs_in[][13]<br/>OTR, temperature, kla<br/>upstreamReactor link<br/>updateState&#40;newTime&#41;<br/>_connectMeasurement / _connectReactor"]
-    end
-    subgraph cstr["Reactor_CSTR"]
-        cs["state = number[13]<br/>tick&#40;dt&#41;:<br/>  inflow + outflow + reaction + transfer<br/>  Forward Euler<br/>  _capDissolvedOxygen / _arrayClip2Zero"]
-    end
-    subgraph pfr["Reactor_PFR"]
-        ps["state = number[n_x][13]<br/>length, n_x, d_x, A, alpha, D<br/>D_op / D2_op finite-difference operators<br/>tick&#40;dt&#41;:<br/>  dispersion + advection + reaction + transfer<br/>  Explicit FD<br/>  Danckwerts inlet / Neumann outlet BC<br/>  Peclet / Courant guard warnings"]
-    end
-    bs --> cs
-    bs --> ps
-```
-
-### Forward Euler (CSTR)
-
-`Reactor_CSTR.tick(time_step)` adds four contributions per step:
-
-| Term | Formula | Notes |
-|:---|:---|:---|
-| Inflow | `Fs &middot; Cs_in / volume` | Per inlet, summed into a single concentration delta. |
-| Outflow | `&minus;sum(Fs) / volume &middot; state` | Mass leaves at the current tank concentration. |
-| Reaction | `asm.compute_dC(state, T)` | ASM3 rate vector applied at current temperature. |
-| Transfer | `OTR or kla &middot; (sat(T) &minus; S_O)` on the `S_O` index only | All other species: zero transfer. |
-
-After integration, `_capDissolvedOxygen` caps `S_O` to saturation and `_arrayClip2Zero` floors negative concentrations.
-
-### Explicit FD (PFR)
-
-`Reactor_PFR.tick(time_step)` operates per grid cell:
-
-| Term | Notes |
-|:---|:---|
-| Dispersion | `(D / d_x²) &middot; D2_op &middot; state` &mdash; central-difference second-derivative operator. |
-| Advection | `(&minus;sum(Fs) / (A &middot; d_x)) &middot; D_op &middot; state` &mdash; first-derivative operator (central or upwind per config). |
-| Reaction | Per-cell `asm.compute_dC(slice, T)`. |
-| Transfer | OTR / `kla` on the `S_O` index, scaled by `n_x / (n_x &minus; 2)` for interior cells only. |
-
-Boundary conditions: **Danckwerts** at the inlet when `sum(Fs) > 0` (mixes inlet concentration with diffusive back-mix governed by `alpha`); **Neumann** (no-flux) at the outlet and at the inlet when there is no flow. After integration, the same `_capDissolvedOxygen` / `_arrayClip2Zero` post-processing applies cell-by-cell.
-
-`updateState` extends `BaseReactorEngine.updateState` with two stability checks:
-
-| Check | Threshold | Warning |
-|:---|:---|:---|
-| Local Peclet `Pe = d_x &middot; sum(Fs) / (D &middot; A)` | `&ge; 2` | `Local Peclet number (&hellip;) is too high! Increase reactor resolution.` |
-| Courant `Co_D = D &middot; timeStep / d_x²` | `&ge; 0.5` | `Courant number (&hellip;) is too high! Reduce time step size.` |
-
----
-
-## Lifecycle &mdash; what one `data.clock` advance does
-
-```mermaid
-sequenceDiagram
-    autonumber
-    participant clock as data.clock injector
-    participant rx as reactor (specificClass)
-    participant engine as kinetics engine (CSTR / PFR)
-    participant downstream as settler / next reactor
-    participant out as Port 0 / 1
-
-    clock->>rx: data.clock { timestamp }
-    rx->>engine: updateState(timestamp)
-    Note over engine: n_iter = floor(speedUpFactor &times; &Delta;t / timeStep)
-    alt upstreamReactor present
-        engine->>engine: setInfluent = upstream.getEffluent
-    end
-    loop n_iter times
-        engine->>engine: tick(timeStep) &mdash; integrate ASM3 rates
-        engine->>engine: cap S_O to saturation, clip negatives
-    end
-    engine->>rx: emit 'stateChange' (currentTime)
-    rx->>rx: re-emit 'stateChange' on BaseDomain emitter
-    rx->>rx: notifyOutputChanged
-    alt PFR engine
-        rx->>out: Port 0 &mdash; GridProfile { grid, n_x, d_x, length, species }
-    end
-    rx->>out: Port 0 &mdash; Fluent { inlet=0, F, C[13] }
-    rx->>out: Port 1 &mdash; InfluxDB scalars { flow_total, temperature, S_O&hellip;X_TS }
-    downstream-->>rx: subscribes to stateChange via _connectReactor
-    downstream->>downstream: pulls getEffluent on each stateChange
-```
-
-The tick loop is opt-in (`static tickInterval = 1000`) because the integrator advances **process time** in steps that have no fixed wall-clock mapping. Without ticks the engine simply doesn't advance. `nodeClass._emitOutputs` is overridden so the `Fluent` / `GridProfile` envelope shape survives the BaseNodeAdapter pipeline.
-
----
-
-## Child registration
-
-Source: `src/specificClass.js` `configure()` wires the ChildRouter; `BaseReactorEngine._connectMeasurement` and `_connectReactor` do the actual subscription.
-
-```mermaid
-flowchart LR
-    subgraph kids["accepted children (softwareType)"]
-        m_t["measurement<br/>asset.type=temperature<br/>positionVsParent=atEquipment"]:::ctrl
-        m_o["measurement<br/>asset.type=quantity (oxygen)<br/>positionVsParent=numeric distance (PFR)"]:::ctrl
-        r_up["reactor<br/>positionVsParent=upstream"]:::unit
-    end
-    m_t -->|temperature.measured.atEquipment| h_meas["engine._connectMeasurement<br/>(baseEngine.js)"]
-    m_o -->|quantity(oxygen).measured.&lt;distance&gt;| h_meas
-    r_up -.stateChange.-> h_react["engine._connectReactor<br/>(baseEngine.js)"]
-    h_meas --> reconcile["reconcile T &rarr; engine.temperature<br/>reconcile O2 &rarr; state grid cell (PFR only)"]
-    h_react --> pull["pull upstream getEffluent<br/>&rarr; Fs[0] / Cs_in[0] before next tick"]
-    classDef ctrl fill:#a9daee,color:#000
-    classDef unit fill:#50a8d9,color:#000
-```
-
-### `_connectMeasurement` event wiring
-
-`measurement.measurements.emitter` fires `<measurementType>.measured.<position>` on every published value. The reactor subscribes:
-
-```js
-const eventName = `${measurementType}.measured.${position}`;
-measurement.measurements.emitter.on(eventName, (eventData) => {
-  this.measurements
-    .type(measurementType).variant('measured').position(position)
-    .value(eventData.value, eventData.timestamp, eventData.unit);
-  this._updateMeasurement(measurementType, eventData.value, position, eventData);
-});
-```
-
-`_updateMeasurement` (CSTR base): only `temperature` at `POSITIONS.AT_EQUIPMENT` is honoured &mdash; writes `engine.temperature`. Any other type logs `Type '<x>' not recognized for measured update.`
-
-`_updateMeasurement` (PFR override): additionally handles `quantity (oxygen)` at a **numeric** position. Position is interpreted as metres along `length`; the value is written to grid cell `clamp(round(pos / length &times; n_x), 0, n_x &minus; 1)`. Non-finite position / value, or `length &le; 0`, logs a warn and the update is dropped.
-
-### `_connectReactor` &mdash; upstream chain
-
-Setting `positionVsParent: 'upstream'` on the upstream reactor's child-register makes this reactor subscribe to the upstream's `stateChange`. On every event the downstream's `updateState` runs, which first pulls the upstream's `getEffluent` into `Fs[0]` / `Cs_in[0]` then integrates.
-
-> [!NOTE]
-> `diffuser` is **not** a registered child. It feeds aeration via the `data.otr` topic on Port 0 (handled in `commands/handlers.js` `dataOTR`). No child-registration handshake.
-
----
-
-## Output ports
-
-| Port | Carries | Sample shape |
-|:---|:---|:---|
-| 0 (process) | `Fluent` envelope every advance. For PFR: an additional `GridProfile` message sent **before** the `Fluent`. | `{topic: 'Fluent', payload: {inlet: 0, F, C: [...13...]}, timestamp}` |
-| 1 (telemetry) | InfluxDB line-protocol payload built from `getOutput()` via `outputUtils.formatMsg`. Fields: `flow_total`, `temperature`, and one per species. | `reactor,id=rx_a flow_total=1000,temperature=20,S_O=2.1,S_NH=0.8,...` |
-| 2 (registration) | `child.register` upward at init | `{topic: 'child.register', payload: <node.id>, positionVsParent, distance}` |
-
-<!-- BEGIN AUTOGEN: data-model — populate via wiki-gen tool (TODO) -->
-
-> [!NOTE]
-> Pending full node review (2026-05). The flat Port-1 telemetry shape (one field per species, plus `flow_total` + `temperature`) reflects the current `getOutput()` in `src/specificClass.js`.
-
-| Key | Type | Unit | Source |
-|:---|:---|:---|:---|
-| `flow_total` | number | m³/d | `sum(Fs)` from the engine's effluent envelope |
-| `temperature` | number | &deg;C | `engine.temperature` |
-| `S_O` | number | mg/L | effluent `C[0]` &mdash; dissolved oxygen, capped to saturation |
-| `S_I` | number | mg/L | effluent `C[1]` &mdash; inert soluble COD |
-| `S_S` | number | mg/L | effluent `C[2]` &mdash; readily biodegradable substrate |
-| `S_NH` | number | mg/L | effluent `C[3]` &mdash; ammonium nitrogen |
-| `S_N2` | number | mg/L | effluent `C[4]` &mdash; dinitrogen |
-| `S_NO` | number | mg/L | effluent `C[5]` &mdash; nitrate / nitrite |
-| `S_HCO` | number | mmol/L | effluent `C[6]` &mdash; alkalinity |
-| `X_I` | number | mg/L | effluent `C[7]` &mdash; inert particulate COD |
-| `X_S` | number | mg/L | effluent `C[8]` &mdash; slowly biodegradable substrate |
-| `X_H` | number | mg/L | effluent `C[9]` &mdash; heterotrophic biomass |
-| `X_STO` | number | mg/L | effluent `C[10]` &mdash; stored COD in biomass |
-| `X_A` | number | mg/L | effluent `C[11]` &mdash; autotrophic biomass |
-| `X_TS` | number | mg/L | effluent `C[12]` &mdash; total suspended solids |
-
-<!-- END AUTOGEN: data-model -->
-
-### Status badge
-
-Composed by `getStatusBadge()` in `src/specificClass.js`:
-
-```
-<EngineType>  T=<temperature> C  F=<flow> m³/d  S_O=<S_O> mg/L
-```
-
-Engine type is `CSTR` or `PFR` (derived from the constructor name). Fill is green by default; the badge is purely informational &mdash; no shape / colour transitions tied to plant state, since reactor has no FSM.
-
----
-
-## Event sources
-
-| Source | Where it fires | What it triggers |
-|:---|:---|:---|
-| `engine.emitter` `'stateChange'` | `BaseReactorEngine.updateState` after `n_iter > 0` integration steps | `specificClass` re-emits on `this.emitter`; BaseNodeAdapter `_emitOutputs` runs (Port 0 + Port 1) |
-| Child measurement emitter | `measurement.measurements.emitter` per `<type>.measured.<position>` | `engine._connectMeasurement` callback &rarr; writes into MeasurementContainer + `_updateMeasurement` reconcile |
-| Upstream reactor `'stateChange'` | Upstream reactor's `BaseDomain` emitter | `engine._connectReactor` callback &rarr; downstream `updateState(t)` runs, pulling upstream effluent first |
-| Inbound `msg.topic` | Node-RED input wire | `commandRegistry` dispatch |
-| `setInterval(tickInterval = 1000)` | `BaseNodeAdapter` periodic tick | `nodeClass._emitOutputs` &rarr; `source.updateState(Date.now())` + send |
-| `setInterval(statusInterval = 1000)` | `BaseNodeAdapter` | Status badge re-render |
-
----
-
-## Where to start reading
-
-| If you're changing&hellip; | Read first |
-|:---|:---|
-| ASM3 stoichiometry / kinetic constants | `src/reaction_modules/asm3_class.js` |
-| Mixed-tank integration, child wiring, influent / OTR / T setters | `src/kinetics/baseEngine.js`, `src/kinetics/cstr.js` |
-| Plug-flow discretization, dispersion, grid profile | `src/kinetics/pfr.js` |
-| Topic registration, alias deprecation | `src/commands/index.js`, `src/commands/handlers.js` |
-| Editor-field &harr; engine-config mapping | `src/nodeClass.js` `buildDomainConfig`, `src/specificClass.js` `_flattenEngineConfig` |
-| Port-0 envelope shape (`Fluent` + `GridProfile`) | `src/nodeClass.js` `_emitOutputs` |
-| Schema defaults, types, units | `generalFunctions/src/configs/reactor.json` |
-
----
-
-## Related pages
-
-| Page | Why |
-|:---|:---|
-| [Home](Home) | Intuitive overview |
-| [Reference &mdash; Contracts](Reference-Contracts) | Topic + config + child filters |
-| [Reference &mdash; Examples](Reference-Examples) | Shipped flows + debug recipes |
-| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
-| [settler wiki](https://gitea.wbd-rd.nl/RnD/settler/wiki/Home) | The typical downstream Unit that subscribes to reactor `stateChange` |
-| [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home) | The Equipment node that pushes `data.otr` |
-| [EVOLV &mdash; Architecture](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Architecture) | Platform-wide three-tier pattern |

wiki/Reference-Contracts.md

@@ -1,227 +0,0 @@
-# Reference — Contracts
-
-![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
-
-> [!NOTE]
-> Full topic contract, configuration schema, and child-registration filters for `reactor`. Source of truth: `src/commands/index.js`, `src/specificClass.js` `configure()`, and the schema at `generalFunctions/src/configs/reactor.json`.
->
-> Pending full node review (2026-05). Content reflects `CONTRACT.md` and current source only.
->
-> For an intuitive overview, return to the [Home](Home).
-
----
-
-## Topic contract
-
-The registry lives in `src/commands/index.js`. Each descriptor maps a canonical `msg.topic` to its handler; aliases emit a one-time deprecation warning the first time they fire.
-
-<!-- BEGIN AUTOGEN: topic-contract -->
-
-| Canonical topic | Aliases | Payload | Unit | Effect |
-|---|---|---|---|---|
-| `data.clock` | `clock` | any | — | Push the simulation clock tick (timestamp / dt) to the ASM solver. |
-| `data.fluent` | `Fluent` | `object` | — | Push the influent stream (payload: {F: flow m3/h, C: [concentrations mg/L]}). |
-| `data.otr` | `OTR` | any | — | Push the current oxygen-transfer rate into the reactor. |
-| `data.temperature` | `Temperature` | any | — | Push the current reactor temperature. |
-| `data.dispersion` | `Dispersion` | any | — | Push a dispersion/mixing parameter update. |
-| `child.register` | `registerChild` | any | — | Register a child node (settler / measurement) with this reactor. |
-
-<!-- END AUTOGEN: topic-contract -->
-
-### Modes / sources / actions
-
-reactor has **no mode, no action allow-lists, no source gating**. All topics are accepted as long as the payload shape is valid. (Contrast with `rotatingMachine`, which gates every input through a mode &times; source matrix.)
-
----
-
-## Data model &mdash; `getOutput()` shape
-
-Composed each tick by `src/specificClass.js` `getOutput()`. Used to build the Port-1 InfluxDB payload; Port 0 carries the engine's `getEffluent` envelope directly.
-
-### Port-0 process payload
-
-The engine's effluent envelope, emitted on every successful `updateState` advance:
-
-```json
-{
-  "topic": "Fluent",
-  "payload": { "inlet": 0, "F": <m³/d>, "C": [<13 species, mg/L>] },
-  "timestamp": <ms since epoch>
-}
-```
-
-For a PFR an additional message is sent **before** the `Fluent` on the same port each advance:
-
-```json
-{
-  "topic": "GridProfile",
-  "payload": {
-    "grid": [[<13 cells of n_x>]],
-    "n_x": <int>,
-    "d_x": <m>,
-    "length": <m>,
-    "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": <ms since epoch>
-  }
-}
-```
-
-### Port-1 telemetry &mdash; scalar keys
-
-| Key | Type | Unit | Source |
-|:---|:---|:---|:---|
-| `flow_total` | number | m³/d | `sum(Fs)` from effluent envelope |
-| `temperature` | number | &deg;C | `engine.temperature` |
-| `S_O` | number | mg/L | effluent `C[0]` &mdash; capped to saturation by `_capDissolvedOxygen` |
-| `S_I` | number | mg/L | effluent `C[1]` |
-| `S_S` | number | mg/L | effluent `C[2]` |
-| `S_NH` | number | mg/L | effluent `C[3]` |
-| `S_N2` | number | mg/L | effluent `C[4]` |
-| `S_NO` | number | mg/L | effluent `C[5]` |
-| `S_HCO` | number | mmol/L | effluent `C[6]` &mdash; alkalinity |
-| `X_I` | number | mg/L | effluent `C[7]` |
-| `X_S` | number | mg/L | effluent `C[8]` |
-| `X_H` | number | mg/L | effluent `C[9]` |
-| `X_STO` | number | mg/L | effluent `C[10]` |
-| `X_A` | number | mg/L | effluent `C[11]` |
-| `X_TS` | number | mg/L | effluent `C[12]` |
-
-Non-finite species values are **omitted** from the output (the `Number.isFinite` guard in `getOutput`); they are not emitted as `null`. Pick one convention per consumer (absent vs null) and document it &mdash; see `.claude/rules/output-coverage.md`.
-
-### Species ordering
-
-The 13-species vector is **fixed**:
-
-| Index | Key | Group |
-|:---:|:---|:---|
-| 0 | `S_O` | soluble |
-| 1 | `S_I` | soluble |
-| 2 | `S_S` | soluble |
-| 3 | `S_NH` | soluble |
-| 4 | `S_N2` | soluble |
-| 5 | `S_NO` | soluble |
-| 6 | `S_HCO` | soluble |
-| 7 | `X_I` | particulate |
-| 8 | `X_S` | particulate |
-| 9 | `X_H` | particulate |
-| 10 | `X_STO` | particulate |
-| 11 | `X_A` | particulate |
-| 12 | `X_TS` | particulate |
-
-Don't reshuffle &mdash; `getOutput()` and `_flattenEngineConfig()` both depend on this exact order, as does `additional_nodes/settling-basin` and the downstream `settler` node.
-
-### Status badge
-
-`getStatusBadge()` in `src/specificClass.js`:
-
-```
-<EngineType>  T=<°C>.X C  F=<m³/d>.XX m³/d  S_O=<mg/L>.XX mg/L
-```
-
-Engine type is the constructor name with `Reactor_` stripped (so `CSTR` or `PFR`). Badge is always green-dot (no FSM-driven state).
-
----
-
-## Configuration schema &mdash; editor form to config keys
-
-Source of truth: `generalFunctions/src/configs/reactor.json` plus `nodeClass.buildDomainConfig` (`src/nodeClass.js`).
-
-### General (`config.general`)
-
-| Form field | Config key | Default | Notes |
-|:---|:---|:---|:---|
-| Name | `general.name` | `Reactor` | Human-readable. |
-| (auto-assigned) | `general.id` | `null` | Node-RED node id. |
-| Default unit | `general.unit` | `null` | Unused by the reactor's own logic (the engines pick up units from the schema's `rules.unit` strings); kept for parent compatibility. |
-| Log enabled | `general.logging.enabled` | `true` | Master switch. |
-| Log level | `general.logging.logLevel` | `info` | `debug` / `info` / `warn` / `error`. |
-
-### Functionality (`config.functionality`)
-
-| Form field | Config key | Default | Notes |
-|:---|:---|:---|:---|
-| Position vs parent | `functionality.positionVsParent` | `atEquipment` | Used in the child-register payload that goes UP to whatever parent registers this reactor. Enum: `upstream` / `atEquipment` / `downstream`. |
-| (hidden) | `functionality.softwareType` | `reactor` | Constant. |
-| (hidden) | `functionality.role` | `Biological reactor for wastewater treatment` | Constant. |
-
-### Reactor (`config.reactor`)
-
-| Form field | Config key | Schema default | Range / unit | Notes |
-|:---|:---|:---|:---|:---|
-| Reactor type | `reactor.reactor_type` | `CSTR` | enum: `CSTR` / `PFR` | Selected once at `configure()`. `_buildEngine` calls `.toUpperCase()` so `pfr` and `PFR` both resolve. |
-| Volume | `reactor.volume` | `1000` | m³, `> 0` | Used by mass balance and (PFR) surface-area derivation. |
-| Length | `reactor.length` | `10` | m, `> 0` | **PFR only.** Sets axial extent and grid pitch (`d_x = length / n_x`). |
-| Resolution | `reactor.resolution_L` | `10` | integer `&ge; 1` | **PFR only.** Grid cell count `n_x`. |
-| Alpha | `reactor.alpha` | `0.5` | `0..1` | **PFR only.** Inlet boundary blend: `0` = pure Danckwerts, `1` = fully mixed inlet. |
-| Inlets | `reactor.n_inlets` | `1` | integer `&ge; 1` | `Fs[]` / `Cs_in[]` array size. |
-| kLa | `reactor.kla` | `0` | 1/h, `&ge; 0`; set `NaN` to disable | Enables internal aeration `OTR = kla &middot; (sat(T) &minus; S_O)`. When `NaN`, `data.otr` is honoured instead. |
-| Time step | `reactor.timeStep` | `0.001` | `&ge; 0.0001` | Schema declares unit `h`; `baseEngine.js` converts by `&divide; 86400` (treating it as seconds). See [Limitations &mdash; timeStep unit mismatch](Reference-Limitations#timestep-unit-mismatch). |
-| Speed-up factor | `reactor.speedUpFactor` | `1` | `&ge; 1` | Multiplies wall-clock &Delta;t when computing `n_iter`. `2` means twice as many internal steps per second. |
-
-### Initial state (`config.initialState`)
-
-13 starting concentrations, all written into the engine's `state` (CSTR: single row; PFR: replicated across all `n_x` grid cells at construction).
-
-| Form field | Config key | Schema default | HTML default | Unit | Notes |
-|:---|:---|:---|:---|:---|:---|
-| Initial S_O | `initialState.S_O` | `0` | check editor | mg/L | Capped to saturation on the first tick. |
-| Initial S_I | `initialState.S_I` | `30` | check editor | mg/L | Inert soluble COD. |
-| Initial S_S | `initialState.S_S` | `70` | check editor | mg/L | Readily biodegradable substrate. |
-| Initial S_NH | `initialState.S_NH` | `25` | check editor | mg/L | Ammonium &mdash; declines with nitrification. |
-| Initial S_N2 | `initialState.S_N2` | `0` | check editor | mg/L | Dinitrogen. |
-| Initial S_NO | `initialState.S_NO` | `0` | check editor | mg/L | Nitrate / nitrite. |
-| Initial S_HCO | `initialState.S_HCO` | `5` | check editor | mmol/L | Alkalinity. |
-| Initial X_I | `initialState.X_I` | `1000` | check editor | mg/L | Inert particulate COD. |
-| Initial X_S | `initialState.X_S` | `100` | check editor | mg/L | Slowly biodegradable substrate. |
-| Initial X_H | `initialState.X_H` | `2000` | check editor | mg/L | Heterotrophic biomass. |
-| Initial X_STO | `initialState.X_STO` | `0` | check editor | mg/L | Stored COD in biomass. |
-| Initial X_A | `initialState.X_A` | `200` | **`0.001`** | mg/L | **Footgun.** HTML default in `reactor.html` (per `CONTRACT.md`) is effectively zero, disabling nitrification. Always verify the deployed form value. |
-| Initial X_TS | `initialState.X_TS` | `3500` | check editor | mg/L | Total suspended solids &mdash; drives downstream settler split. |
-
-> [!WARNING]
-> The HTML form supplies its own defaults; for fields where they differ from the schema (notably `X_A`), the HTML wins at deploy time. Either match the schema in the HTML or audit every deployed flow.
-
-### Unit policy
-
-reactor does **not** declare a UnitPolicy in `specificClass`. Units are carried in the schema's `rules.unit` strings (m³, m, 1/h, mg/L, mmol/L) and consumed by the engines without normalisation through MeasurementContainer's canonical-unit rule. Notable internal conversions:
-
-| Quantity | What the engine uses internally | Where converted |
-|:---|:---|:---|
-| `timeStep` | days | `baseEngine.js` line ~40: `timeStep = config.timeStep / 86400` |
-| `Fs` | m³/d (assumed by mass-balance formulas) | not converted &mdash; the caller is expected to push m³/d on `data.fluent` |
-| `temperature` | &deg;C | stored as supplied (Celsius); `_calcOxygenSaturation(T)` expects &deg;C |
-
-This is a known divergence from the platform-wide canonical-unit rule (`Pa` / `m³/s` / `W` / `K`). Tracked.
-
----
-
-## Child registration
-
-Source: `src/specificClass.js` `configure()` (ChildRouter wiring) + `BaseReactorEngine._connectMeasurement` / `_connectReactor`.
-
-| Software type | Filter | Wired to | Side-effect |
-|:---|:---|:---|:---|
-| `measurement` | `asset.type = 'temperature'`, `positionVsParent = atEquipment` | `engine._connectMeasurement` &rarr; `_updateMeasurement` | Writes `engine.temperature`. CSTR only honours this. |
-| `measurement` | `asset.type = 'quantity (oxygen)'`, `positionVsParent = <numeric distance>` | `engine._connectMeasurement` &rarr; `Reactor_PFR._updateMeasurement` | **PFR only.** Maps measurement to nearest grid cell by `clamp(round(pos / length &times; n_x), 0, n_x &minus; 1)`. Writes into `state[cell][S_O_INDEX]`. |
-| `reactor` | `positionVsParent = 'upstream'` | `engine._connectReactor` | Subscribes to upstream reactor's `stateChange`. Each event triggers downstream `updateState`, which pulls upstream `getEffluent` into `Fs[0]` / `Cs_in[0]` before integrating. |
-
-### Not a child: `diffuser`
-
-`diffuser` (Equipment Module) is **not** registered as a reactor child. It feeds aeration via the `data.otr` topic on Port 0. No child-registration handshake is involved. If you want the diffuser's OTR to drive the reactor, wire the diffuser's process output to the reactor's input directly.
-
-### Unrecognised softwareType
-
-`BaseReactorEngine.registerChild` logs `Unrecognized softwareType: <x>` and drops the registration. There is no `valve`, `rotatingMachine`, etc. acceptance path.
-
----
-
-## Related pages
-
-| Page | Why |
-|:---|:---|
-| [Home](Home) | Intuitive overview |
-| [Reference &mdash; Architecture](Reference-Architecture) | Code map, integration sequence, kinetics |
-| [Reference &mdash; Examples](Reference-Examples) | Shipped flows + debug recipes |
-| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
-| [EVOLV &mdash; Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions) | Platform-wide topic rules |
-| [EVOLV &mdash; Telemetry](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Telemetry) | Port 0 / 1 / 2 InfluxDB layout |

wiki/Reference-Examples.md

@@ -1,160 +0,0 @@
-# Reference — Examples
-
-![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
-
-> [!NOTE]
-> Every example flow shipped under `nodes/reactor/examples/`, plus how to load them, what they show, and the debug recipes that go with them. Live source: `nodes/reactor/examples/`.
->
-> Pending full node review (2026-05). The current flows predate the standard 3-tier example-flow rework that `rotatingMachine` has completed; planned upgrade is tracked in the EVOLV superproject memory ("Example Flows" TODO).
-
----
-
-## Shipped examples
-
-| File | Tier | Dependencies | What it shows |
-|:---|:---:|:---|:---|
-| `basic.flow.json` | 1 | EVOLV only | Single CSTR with one inlet. Inject `data.fluent` to set influent, `data.clock` to advance the integrator; watch `Fluent` effluent on Port 0 and InfluxDB scalars on Port 1. |
-| `integration.flow.json` | 2 | EVOLV only | Upstream `reactor` → `reactor` → `settler` chain. The downstream reactor registers the upstream via `child.register positionVsParent=upstream`; on each upstream `stateChange` the downstream pulls effluent and advances. |
-| `edge.flow.json` | 3 | EVOLV only | PFR with axial dispersion (`data.dispersion`) and multi-inlet (`n_inlets > 1`). Emits both `GridProfile` and `Fluent` per advance. |
-
-> [!IMPORTANT]
-> **Screenshots needed.** Editor capture of each example flow. Save as `wiki/_partial-screenshots/reactor/{01-basic-cstr,02-chain,03-pfr-edge}.png`. Replace these callouts with image links once captured.
-
-The legacy `additional_nodes/recirculation-pump` and `additional_nodes/settling-basin` Node-RED nodes are shipped from this repo but are not yet refactored to BaseDomain — they aren't part of these examples.
-
----
-
-## Loading a flow
-
-### Via the editor
-
-1. Open the Node-RED editor at `http://localhost:1880`.
-2. Menu → Import → drag the JSON file.
-3. Click Deploy.
-
-### Via the Admin API
-
-```bash
-curl -X POST -H 'Content-Type: application/json' \
-  --data @nodes/reactor/examples/basic.flow.json \
-  http://localhost:1880/flows
-```
-
----
-
-## Example — Basic CSTR
-
-Single-reactor flow with one inlet and the minimum set of inputs needed to drive nitrification.
-
-### What to do after deploy
-
-1. Inject `data.temperature` with `payload: 15` (or whatever process T you want). Optional — default is 20 °C.
-2. Inject `data.fluent` with:
-   ```json
-   {
-     "topic": "data.fluent",
-     "payload": {
-       "inlet": 0,
-       "F": 1000,
-       "C": [0, 30, 70, 25, 0, 0, 5, 1000, 100, 2000, 0, 200, 3500]
-     }
-   }
-   ```
-   Note `C[11] = 200` (X_A — autotroph biomass). If you copy the HTML default of `0.001`, nitrification never starts.
-3. If `kla > 0` is configured, you can skip OTR injection; the engine aerates internally. Otherwise inject `data.otr` with a positive scalar.
-4. Inject `data.clock` repeatedly (or rely on the periodic tick — `tickInterval = 1000` ms wall-clock). Each advance integrates `n_iter = floor(speedUpFactor · Δt / timeStep_days)` internal steps.
-5. Watch the debug tap on Port 0: `Fluent` envelopes with the 13-species effluent. `S_NH` should fall, `S_NO` should rise — nitrification is proceeding.
-
-> [!IMPORTANT]
-> **GIF needed.** Demo recording of `S_NH` ↓ / `S_NO` ↑ over 30 simulated days. Save as `wiki/_partial-gifs/reactor/01-basic-cstr.gif`.
-
----
-
-## Example — Reactor chain
-
-Upstream → downstream coupling demo. The downstream reactor registers the upstream via:
-
-```json
-{
-  "topic": "child.register",
-  "payload": "<upstream-reactor-node-id>",
-  "positionVsParent": "upstream"
-}
-```
-
-On every upstream `stateChange`, `engine._connectReactor` triggers downstream `updateState`. That call first reads `upstream.getEffluent` into the downstream's `Fs[0]` / `Cs_in[0]`, then integrates. So one `data.clock` to the upstream advances the whole chain.
-
-> [!NOTE]
-> Pending full node review (2026-05). The flow currently in `integration.flow.json` may not yet conform to the multi-tab layout standard (Process Plant / Dashboard UI / Demo Drivers / Setup) described in `.claude/rules/node-red-flow-layout.md` &mdash; planned upgrade tracked in the EVOLV "Example Flows" TODO.
-
----
-
-## Example &mdash; PFR edge
-
-Plug-flow reactor with axial discretization. After deploy:
-
-1. Inject `data.dispersion` with `payload: <m²/d>` to set the axial dispersion coefficient `D`.
-2. Inject one or more `data.fluent` messages with distinct `inlet` indices (0..`n_inlets &minus; 1`).
-3. Drive with `data.clock` as usual.
-4. Watch Port 0: each advance emits a `GridProfile` **before** the `Fluent`. The grid has `n_x` rows, 13 columns each.
-5. Add a `measurement` child with `asset.type = 'quantity (oxygen)'` and a numeric `positionVsParent` (e.g. `5` for 5 m from the inlet). On each measurement event the PFR engine writes the value into the nearest grid cell's `S_O`.
-
-Stability tips:
-
-- `Pe_local = d_x &middot; sum(Fs) / (D &middot; A)` must be `< 2` &mdash; if you see `Local Peclet number ... is too high!`, either increase `resolution_L` (more cells, smaller `d_x`) or raise `D`.
-- `Co_D = D &middot; timeStep / d_x²` must be `< 0.5` for the explicit FD scheme &mdash; if you see `Courant number ... is too high!`, decrease `timeStep`.
-
----
-
-## Debug recipes
-
-| Symptom | First thing to check | Where to look |
-|:---|:---|:---|
-| `S_NH` stays at its initial value &mdash; nitrification not proceeding | `initialState.X_A` is effectively zero (HTML default is `0.001` mg/L). Set to `~50` or higher to seed autotrophs. | `reactor.html` &harr; `generalFunctions/src/configs/reactor.json` `initialState.X_A` |
-| `Fluent` payload `F = 0` | No `data.fluent` arrived, or `Fs[0]` is still 0 (no inlet flow). Check the message payload shape: `{inlet, F, C}`. | `src/commands/handlers.js` `dataFluent`, engine `setInfluent` |
-| `Fluent` payload appears, but `C` array is all zeros / unchanged | `data.clock` not arriving, or `n_iter = 0` (timestamp delta too small for the configured `timeStep`). Bump `speedUpFactor` or check that clock injects are firing. | `engine.updateState` in `baseEngine.js` |
-| PFR `GridProfile` not emitted | `reactor.reactor_type` is `CSTR` &mdash; only PFR has a grid profile. | `nodeClass._emitOutputs`, `pfr.getGridProfile` |
-| `temperature` ignored | Payload is non-numeric, or wrapped as `{value: ...}` with `value` non-finite. Look for `Invalid temperature input: <raw>` in the log. | `baseEngine.js` `setTemperature` setter |
-| Temperature child measurement not reconciling | The child's `asset.type` must be exactly `'temperature'` and `positionVsParent = atEquipment`. Anything else logs `Type '<x>' not recognized for measured update.` | `baseEngine.js` `_updateMeasurement` |
-| `Local Peclet number ... is too high!` warning on every PFR `updateState` | Either `D` is too small, or `d_x` is too large. Increase `resolution_L` or set a larger dispersion. | `pfr.updateState` Peclet guard |
-| `Courant number ... is too high!` warning | `timeStep` is too large for the configured `D`. Reduce it. | `pfr.updateState` Courant guard |
-| Settler downstream not updating | Settler must subscribe to the **reactor's `emitter`**, not `reactor.measurements.emitter`. Historical bug in `settler/src/specificClass.js` `_connectReactor` (fixed 2026-03-02). | upstream chain wiring, `settler._connectReactor` |
-| `wiki:datamodel` autogen script slow / timing out | `mathjs` cold-start is ~13 s. The current 60 s wrapper sometimes times out. | known limitation; fall back to the hand-curated Concrete sample in `CONTRACT.md` `Home.md` |
-| `reactor_type: 'pfr'` (lowercase) silently runs CSTR | Schema validator lowercases the enum; `_buildEngine` calls `.toUpperCase()` to compensate. If you stripped that guard, lowercase `pfr` falls through to the default branch (CSTR). | `src/specificClass.js` `_buildEngine` |
-| `data.otr` value ignored | `reactor.kla > 0`. The engine prefers internal `kla &middot; (sat &minus; S_O)` over external OTR. Set `kla = NaN` to enable external OTR. | `cstr.tick` / `pfr.tick` `klaIsNaN` branch |
-
-> Never ship `enableLog: 'debug'` in a demo &mdash; the kinetics engines log per-step on debug, which fills the container log within seconds.
-
----
-
-## Docker compose snippet
-
-To bring up Node-RED + InfluxDB with EVOLV nodes pre-loaded:
-
-```yaml
-# docker-compose.yml (extract)
-services:
-  nodered:
-    build: ./docker/nodered
-    ports: ['1880:1880']
-    volumes:
-      - ./docker/nodered/data:/data/evolv
-  influxdb:
-    image: influxdb:2.7
-    ports: ['8086:8086']
-```
-
-Full file: [EVOLV/docker-compose.yml](https://gitea.wbd-rd.nl/RnD/EVOLV/src/branch/development/docker-compose.yml).
-
----
-
-## Related pages
-
-| Page | Why |
-|:---|:---|
-| [Home](Home) | Intuitive overview |
-| [Reference &mdash; Contracts](Reference-Contracts) | Topic + config + child filters |
-| [Reference &mdash; Architecture](Reference-Architecture) | Code map, kinetics engines, integration sequence |
-| [Reference &mdash; Limitations](Reference-Limitations) | Known issues and open questions |
-| [settler &mdash; Examples](https://gitea.wbd-rd.nl/RnD/settler/wiki/Reference-Examples) | The typical downstream Unit |
-| [EVOLV &mdash; Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns) | Where reactor fits in a larger plant |

wiki/Reference-Limitations.md

@@ -1,132 +0,0 @@
-# Reference — Limitations
-
-![code-ref](https://img.shields.io/badge/code--ref-0e34403-blue)
-
-> [!NOTE]
-> What `reactor` does not do, current rough edges, and open questions. Open items live in `.agents/improvements/IMPROVEMENTS_BACKLOG.md` and `.claude/refactor/OPEN_QUESTIONS.md` in the superproject.
->
-> Pending full node review (2026-05). Content reflects `CONTRACT.md`, the current source, and a partial walkthrough of `src/kinetics/` — not a full audit.
-
----
-
-## When you would not use this node
-
-| Scenario | Use instead |
-|:---|:---|
-| A passive equalisation tank (no biological reactions, just buffering) | A simple Node-RED buffer / function node — the kinetics engines assume reactions are happening. |
-| A residence-time delay (plug-flow without ASM) | A delay node or custom buffer; the ASM3 13-species machinery + `mathjs` cold-start are overkill. |
-| Aerobic-only contactors where you only need oxygen mass-transfer | An OTR-only model is lighter; ASM3 brings 13 species you'll ignore. |
-| A clarifier / settler | `settler` — reactor has no settling, no sludge thickening, no underflow / overflow split. |
-| A pump / blower / valve | `rotatingMachine` / `valve` — reactor is a process-tank model, not an actuator. |
-| Anaerobic digestion | ASM3 is calibrated for activated sludge under aerobic / anoxic conditions. ADM1 (a separate model family) is the right tool for digesters. |
-
----
-
-## Known limitations
-
-### `X_A` initial default footgun
-
-The HTML editor form's default for initial autotroph biomass is **`0.001` mg/L** (effectively zero). The JSON schema default is `200` mg/L. The HTML wins at deploy time. With `X_A ≈ 0` nitrification never starts — `S_NH` stays at the influent value forever, no `S_NO` is produced.
-
-> [!WARNING]
-> Always open every deployed reactor node and confirm `Initial X_A` is `≥ ~50` mg/L before expecting nitrification. Tracked in `CONTRACT.md` `## 14` row 2 and in EVOLV memory `MEMORY.md` "Key Integration Gotchas".
-
-### `mathjs` cold-start ~13 s
-
-`baseEngine.js` requires `mathjs`. The first `require('mathjs')` in a Node.js process takes ~13 s wall-clock to initialise. This delays first `data.clock` advance after a fresh deploy, and can time out the `wiki:datamodel` autogen wrapper (60 s budget). Two remedies tracked:
-
-1. Tree-shake `mathjs` to only the operations actually used (`add`, `multiply`, `diag`, `resize`, `sum`, `divide`).
-2. Lazy-initialise / cache the instance.
-
-Tracked in `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load".
-
-### `timeStep` unit mismatch
-
-- HTML form label: `Time step [s]`.
-- Schema (`generalFunctions/src/configs/reactor.json` line ~144): `unit: "h"`.
-- `baseEngine.js` line ~40 converts by `÷ 86400` (seconds → days) before using it.
-
-The conversion suggests the **true** unit is seconds. Schema is wrong. Until reconciled, treat the form field as seconds. Tracked in `CONTRACT.md` `## 14` row 7 and in `OPEN_QUESTIONS.md` (Phase 5/6 cleanup list).
-
-### `reactor_type` enum casing
-
-The JSON schema validator lowercases `reactor_type` (so `'PFR'` → `'pfr'`). `Reactor._buildEngine` calls `.toUpperCase()` to compensate. If that guard is ever removed prematurely (before the platform-wide canonical casing rule is decided in Phase 7), PFR configs silently fall back to the default branch — which constructs a CSTR. Tracked in `OPEN_QUESTIONS.md`.
-
-### `getEffluent` shape historically varied
-
-Earlier versions of `BaseReactorEngine.getEffluent` returned either an envelope object or an array of envelopes (multi-outlet PFR). The current code emits a single `{topic, payload, timestamp}` envelope, but the downstream `settler._connectReactor` tolerates **both** shapes. Don't break this contract without coordinating with the settler node. EVOLV memory records a 2026-03-02 fix in settler for the array-vs-envelope assumption.
-
-### No FSM — no mode / setpoint / startup-shutdown sequencing
-
-reactor has no startup, no shutdown, no e-stop, no mode, no setpoint. It runs continuous-state ODE / PDE integration unconditionally as long as `data.clock` advances (or the tick loop fires). A downstream consumer that expects a `state` field on Port 0 will get nothing of the sort. This is by design — biological reactors don't have meaningful FSM states — but it's a divergence from `rotatingMachine` / `pumpingStation` patterns that callers should know about.
-
-### No mode / source / action allow-list gating
-
-All incoming topics are accepted as long as the payload validates. There is no `parent` / `GUI` / `fysical` source-gating, no `auto` / `virtualControl` / `fysicalControl` mode-gating. If you want to lock down a deployed reactor (e.g. ignore manual `data.fluent` injections while a real flow sensor is wired), you must do it externally.
-
-### `additional_nodes/` legacy companions not refactored
-
-`additional_nodes/recirculation-pump.js` and `additional_nodes/settling-basin.js` are sibling Node-RED nodes shipped from the reactor repo (because they share the same package context). They are **not yet refactored to BaseDomain**. Tracked as P6.5 follow-up.
-
-### `reaction_modules/` legacy directory
-
-`src/reaction_modules/asm3_class.js` is consumed by the current engines. `src/reaction_modules/asm3_class Koch.js` is a legacy plug-in variant **not consumed by anything in the current codebase**. Removal pending. Tracked as P6.5 follow-up.
-
-### Units don't follow EVOLV canonical-unit rule
-
-The platform-wide MeasurementContainer canonical units are `Pa` / `m³/s` / `W` / `K`. reactor uses m³/d for flow, °C for temperature, mg/L (or mmol/L for alkalinity) for concentrations. No conversion at the system boundary. Calling code that expects canonical units must convert.
-
-### `data.dispersion` is silently a no-op on CSTR
-
-`specificClass.set setDispersion` checks `if (this.engine instanceof Reactor_PFR)` before forwarding. On a CSTR the setter just drops the payload — no warn, no error. If you deploy a flow that injects `data.dispersion` and switch the reactor type to CSTR, the injection is silently ignored.
-
-### Single output-shape convention not documented per-key
-
-The `getOutput()` implementation **omits** non-finite species values (`Number.isFinite` guard) rather than emitting them as `null`. Per `.claude/rules/output-coverage.md`, every node should pick one convention and document it. reactor's is "absent" — downstream consumers should treat a missing species key as "not produced this tick", never as zero.
-
-### `output-coverage` manifest not yet present
-
-`test/_output-manifest.md` (required by the platform-wide output-coverage rule, 2026-05-14) is not yet checked in for reactor. The Port-0 envelope shape, Port-1 InfluxDB fields, and `GridProfile` payload all need enumeration with populated + degraded test coverage. Tracked in `.agents/improvements/IMPROVEMENTS_BACKLOG.md`.
-
----
-
-## Open questions (tracked)
-
-| Question | Where it lives |
-|:---|:---|
-| `mathjs` slow load — tree-shake or lazy-init | `.claude/refactor/OPEN_QUESTIONS.md` — "mathjs slow load" |
-| `reactor_type` enum casing — platform-wide canonical | `.claude/refactor/OPEN_QUESTIONS.md` — "reactor schema enum lowercases reactor_type" |
-| `timeStep` unit reconciliation (HTML `s` vs schema `h` vs engine `d`) | `OPEN_QUESTIONS.md` Phase 5/6 cleanup list |
-| Removal of `reaction_modules/asm3_class Koch.js` and `additional_nodes/*` | P6.5 follow-up |
-| Output-coverage manifest + populated / degraded tests | `.agents/improvements/IMPROVEMENTS_BACKLOG.md` |
-| Should reactor adopt a canonical-unit boundary like the rest of EVOLV? | Internal — not yet ticketed |
-| Multi-outlet PFR (separate effluent streams per spatial point) | Internal — long-term |
-
----
-
-## Migration notes
-
-### From the pre-`BaseDomain` reactor
-
-The current `specificClass` extends `BaseDomain` and uses ChildRouter to dispatch `measurement` / `reactor` registrations. Older flows that pre-date this refactor may have hand-wired child handlers; redeploying after `npm install` should pick up the new path automatically — no schema migration is required.
-
-### From legacy topic names
-
-The five `data.*` topics replace the pre-canonical PascalCase aliases (`Fluent`, `OTR`, `Temperature`, `Dispersion`, `clock`). The aliases are still accepted and emit a one-time deprecation warning on first use, but will be removed in Phase 7. Migrate flows by renaming the topic string on each inject.
-
-### From hand-counted internal steps
-
-Before the `speedUpFactor` field, simulation acceleration required adjusting `timeStep`. The current path is to leave `timeStep` at its physically-meaningful value (~1 s) and crank `speedUpFactor` to advance more process-time per wall-clock second. Old flows with abnormally large `timeStep` should be re-saved with the new field.
-
----
-
-## Related pages
-
-| Page | Why |
-|:---|:---|
-| [Home](Home) | Intuitive overview |
-| [Reference — Contracts](Reference-Contracts) | Topic + config + child filters |
-| [Reference — Architecture](Reference-Architecture) | Code map, kinetics engines, integration sequence |
-| [Reference — Examples](Reference-Examples) | Shipped flows + debug recipes |
-| [settler — Limitations](https://gitea.wbd-rd.nl/RnD/settler/wiki/Reference-Limitations) | The downstream Unit's quirks (incl. the historical `getEffluent` shape tolerance) |
-| [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home) | The Equipment node that pushes `data.otr` — not a registered child |

wiki/_Sidebar.md

@@ -1,20 +0,0 @@
-### reactor
-
-- [Home](Home)
-
-**Reference**
-
-- [Contracts](Reference-Contracts)
-- [Architecture](Reference-Architecture)
-- [Examples](Reference-Examples)
-- [Limitations](Reference-Limitations)
-
-**Related**
-
-- [EVOLV master wiki](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Home)
-- [settler wiki](https://gitea.wbd-rd.nl/RnD/settler/wiki/Home)
-- [diffuser wiki](https://gitea.wbd-rd.nl/RnD/diffuser/wiki/Home)
-- [measurement wiki](https://gitea.wbd-rd.nl/RnD/measurement/wiki/Home)
-- [Topology Patterns](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topology-Patterns)
-- [Topic Conventions](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Topic-Conventions)
-- [Telemetry](https://gitea.wbd-rd.nl/RnD/EVOLV/wiki/Telemetry)